Analyses for Publication

workflowr

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Last updated: 2026-03-19

Checks: 7 0

Knit directory: scSeq_Hefendehl/

This reproducible R Markdown analysis was created with workflowr (version 1.7.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

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Repository version: f7ac121

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    Deleted:    geneviewer/app.R
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File	Version	Author	Date	Message
Rmd	f7ac121	achiocch	2026-03-19	Updated Analysis cluster DEX and GO
html	0d6e2cb	achiocch	2026-03-18	Build site.
Rmd	05a87a1	achiocch	2026-03-18	workflowr::wflow_publish(c("./analysis/sc", "./analysis/index"))

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Load batch 2026

Metadata additional samples

load additonal samples second GT

[1] "scSS2_25_006"
[1] "scSS2_25_007"
[1] "scSS2_25_008"
[1] "scSS2_25_009"
[1] "scSS2_25_11"
[1] "scSS2_25_12"

Load batch 2025

            used  (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells  14296199 763.5   25047220 1337.7  25047220 1337.7
Vcells 121038920 923.5  422946684 3226.9 528673561 4033.5

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 3648
Number of edges: 121160

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7558
Number of communities: 12
Elapsed time: 0 seconds

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

Reclustering of datasets

Define Gene lists

inspect data

SCT CCA integration all cells

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 3228
Number of edges: 91581

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7795
Number of communities: 12
Elapsed time: 0 seconds

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

Sex specific genes

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

remove sex specific and not-annotated genes

Clean integration

Pre cell filtering integration

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 3228
Number of edges: 91581

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7326
Number of communities: 12
Elapsed time: 0 seconds

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Version	Author	Date
0d6e2cb	achiocch	2026-03-18

map cell types

           Adipocytes                 aNSCs            Astrocytes 
                    2                    19                    85 
 Astrocytes activated               B cells        Cardiomyocytes 
                   19                     1                     1 
            Ependymal          Granulocytes           Macrophages 
                    2                    30                    13 
Macrophages activated             Microglia   Microglia activated 
                    2                  2911                    33 
            Monocytes               Neurons     Neurons activated 
                   14                    27                    40 
             NK cells                  NPCs                  OPCs 
                    1                     1                     4 
                qNSCs               T cells 
                    2                    21 

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

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Version	Author	Date
0d6e2cb	achiocch	2026-03-18

filter and recluster only Microglia

Re-optimize clustering

Layer integration across Runs using CCA Integration

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.8331
Number of communities: 4
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.7579
Number of communities: 6
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6942
Number of communities: 6
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6493
Number of communities: 8
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6070
Number of communities: 8
Elapsed time: 0 seconds
Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.5735
Number of communities: 9
Elapsed time: 0 seconds

Define resoultion for clustering

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Version	Author	Date
0d6e2cb	achiocch	2026-03-18

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Version	Author	Date
0d6e2cb	achiocch	2026-03-18

             res1            res2       ARI
1 RNA_snn_res.0.2 RNA_snn_res.0.4 0.4149767
2 RNA_snn_res.0.4 RNA_snn_res.0.6 0.6272156
3 RNA_snn_res.0.6 RNA_snn_res.0.8 0.8785492
4 RNA_snn_res.0.8   RNA_snn_res.1 0.9365022
5   RNA_snn_res.1 RNA_snn_res.1.2 0.7298709

clustering resolultion was set to 0.6

Modularity Optimizer version 1.3.0 by Ludo Waltman and Nees Jan van Eck

Number of nodes: 2944
Number of edges: 108310

Running Louvain algorithm...
Maximum modularity in 10 random starts: 0.6942
Number of communities: 6
Elapsed time: 0 seconds

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0d6e2cb	achiocch	2026-03-18

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0d6e2cb	achiocch	2026-03-18

Map old clusters

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Version	Author	Date
0d6e2cb	achiocch	2026-03-18

            
             Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
  Microglia0         28         94        100        103         52         10
  Microglia1          1         26          3          4          4          2
  Microglia2        128         26          9          3          3          3
  Microglia3          0          0          0          0          0          2
  Microglia4          4          5          1          4          3          0
  Microglia5         12          3          3          0          1          0
            
             Microglia6 Microglia7
  Microglia0         17          1
  Microglia1          0          0
  Microglia2          0          0
  Microglia3          0          0
  Microglia4          0         12
  Microglia5          0          0

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Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Markers for Clusters

--------Summary descriptives table by 'Genotype_Treatment'---------

____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ 
                 WT_Ctrl    WT_Stroke  APPPS1_Ctrl APPPS1_Stroke p.overall p.WT_Ctrl vs WT_Stroke p.WT_Ctrl vs APPPS1_Ctrl p.WT_Ctrl vs APPPS1_Stroke p.WT_Stroke vs APPPS1_Ctrl p.WT_Stroke vs APPPS1_Stroke p.APPPS1_Ctrl vs APPPS1_Stroke 
                  N=827       N=654       N=825        N=638                                                                                                                                                                                 
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
labels:                                                           <0.001           <0.001                  <0.001                      .                        <0.001                      <0.001                        <0.001             
    Microglia0 417 (50.4%) 254 (38.8%) 389 (47.2%)  238 (37.3%)                                                                                                                                                                              
    Microglia1 283 (34.2%) 208 (31.8%) 141 (17.1%)  167 (26.2%)                                                                                                                                                                              
    Microglia2 18 (2.18%)  86 (13.1%)  189 (22.9%)  165 (25.9%)                                                                                                                                                                              
    Microglia3 89 (10.8%)  50 (7.65%)  32 (3.88%)   32 (5.02%)                                                                                                                                                                               
    Microglia4 17 (2.06%)  18 (2.75%)  47 (5.70%)   31 (4.86%)                                                                                                                                                                               
    Microglia5  3 (0.36%)  38 (5.81%)  27 (3.27%)    5 (0.78%)                                                                                                                                                                               
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 

--------Summary descriptives table by 'Genotype_Treatment'---------

__________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ 
               WT_Ctrl    WT_Stroke  APPPS1_Ctrl APPPS1_Stroke p.overall p.WT_Ctrl vs WT_Stroke p.WT_Ctrl vs APPPS1_Ctrl p.WT_Ctrl vs APPPS1_Stroke p.WT_Stroke vs APPPS1_Ctrl p.WT_Stroke vs APPPS1_Stroke p.APPPS1_Ctrl vs APPPS1_Stroke 
                N=827       N=654       N=825        N=638                                                                                                                                                                                 
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
Mouse_ID:                                                        0.000           0.000                   0.000                     0.000                      0.000                       0.000                         0.000              
    256#1022 106 (12.8%)  0 (0.00%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    256#1023 93 (11.2%)   0 (0.00%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    364#469  98 (11.9%)   0 (0.00%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    386       0 (0.00%)  33 (5.05%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    387       0 (0.00%)   0 (0.00%)   0 (0.00%)   28 (4.39%)                                                                                                                                                                               
    388       0 (0.00%)   0 (0.00%)  154 (18.7%)   0 (0.00%)                                                                                                                                                                               
    409       0 (0.00%)  95 (14.5%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    41738     0 (0.00%)   0 (0.00%)   0 (0.00%)   160 (25.1%)                                                                                                                                                                              
    41739     0 (0.00%)   0 (0.00%)   0 (0.00%)   178 (27.9%)                                                                                                                                                                              
    41799     0 (0.00%)  181 (27.7%)  0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    42012     0 (0.00%)  163 (24.9%)  0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    42013     0 (0.00%)   0 (0.00%)   0 (0.00%)   181 (28.4%)                                                                                                                                                                              
    42015    165 (20.0%)  0 (0.00%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    42042     0 (0.00%)  182 (27.8%)  0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    42215    181 (21.9%)  0 (0.00%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    42217    184 (22.2%)  0 (0.00%)   0 (0.00%)    0 (0.00%)                                                                                                                                                                               
    42436     0 (0.00%)   0 (0.00%)  179 (21.7%)   0 (0.00%)                                                                                                                                                                               
    42438     0 (0.00%)   0 (0.00%)  171 (20.7%)   0 (0.00%)                                                                                                                                                                               
    42440     0 (0.00%)   0 (0.00%)  171 (20.7%)   0 (0.00%)                                                                                                                                                                               
    457       0 (0.00%)   0 (0.00%)  150 (18.2%)   0 (0.00%)                                                                                                                                                                               
    461       0 (0.00%)   0 (0.00%)   0 (0.00%)   91 (14.3%)                                                                                                                                                                               
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 

--------Summary descriptives table by 'labels'---------

_____________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________________ 
             Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5 p.overall p.Microglia0 vs Microglia1 p.Microglia0 vs Microglia2 p.Microglia0 vs Microglia3 p.Microglia0 vs Microglia4 p.Microglia0 vs Microglia5 p.Microglia1 vs Microglia2 p.Microglia1 vs Microglia3 p.Microglia1 vs Microglia4 p.Microglia1 vs Microglia5 p.Microglia2 vs Microglia3 p.Microglia2 vs Microglia4 p.Microglia2 vs Microglia5 p.Microglia3 vs Microglia4 p.Microglia3 vs Microglia5 p.Microglia4 vs Microglia5 
               N=1298     N=799      N=458      N=203      N=113       N=73                                                                                                                                                                                                                                                                                                                                                                                                                                   
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 
Mouse_ID:                                                                          .                 .                        <0.001                       .                          .                          .                          .                          .                          .                          .                          .                          .                          .                          .                          .                          .              
    256#1022 59 (4.55%) 29 (3.63%) 3 (0.66%)  11 (5.42%) 3 (2.65%)  1 (1.37%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    256#1023 55 (4.24%) 18 (2.25%) 2 (0.44%)  14 (6.90%) 4 (3.54%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    364#469  69 (5.32%) 19 (2.38%) 3 (0.66%)  2 (0.99%)  4 (3.54%)  1 (1.37%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    386      12 (0.92%) 0 (0.00%)  17 (3.71%) 0 (0.00%)  4 (3.54%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    387      11 (0.85%) 1 (0.13%)  10 (2.18%) 5 (2.46%)  1 (0.88%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    388      52 (4.01%) 17 (2.13%) 53 (11.6%) 2 (0.99%)  8 (7.08%)  22 (30.1%)                                                                                                                                                                                                                                                                                                                                                                                                                                
    409      56 (4.31%) 7 (0.88%)  27 (5.90%) 1 (0.49%)  4 (3.54%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    41738    60 (4.62%) 48 (6.01%) 32 (6.99%) 12 (5.91%) 8 (7.08%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    41739    55 (4.24%) 50 (6.26%) 56 (12.2%) 6 (2.96%)  10 (8.85%) 1 (1.37%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    41799    77 (5.93%) 59 (7.38%) 4 (0.87%)  4 (1.97%)  3 (2.65%)  34 (46.6%)                                                                                                                                                                                                                                                                                                                                                                                                                                
    42012    33 (2.54%) 74 (9.26%) 8 (1.75%)  42 (20.7%) 3 (2.65%)  3 (4.11%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42013    67 (5.16%) 55 (6.88%) 39 (8.52%) 7 (3.45%)  9 (7.96%)  4 (5.48%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42015    99 (7.63%) 53 (6.63%) 4 (0.87%)  7 (3.45%)  1 (0.88%)  1 (1.37%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42042    76 (5.86%) 68 (8.51%) 30 (6.55%) 3 (1.48%)  4 (3.54%)  1 (1.37%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42215    46 (3.54%) 94 (11.8%) 5 (1.09%)  34 (16.7%) 2 (1.77%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42217    89 (6.86%) 70 (8.76%) 1 (0.22%)  21 (10.3%) 3 (2.65%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42436    91 (7.01%) 27 (3.38%) 38 (8.30%) 5 (2.46%)  15 (13.3%) 3 (4.11%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42438    69 (5.32%) 52 (6.51%) 23 (5.02%) 19 (9.36%) 8 (7.08%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    42440    88 (6.78%) 43 (5.38%) 20 (4.37%) 6 (2.96%)  14 (12.4%) 0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    457      89 (6.86%) 2 (0.25%)  55 (12.0%) 0 (0.00%)  2 (1.77%)  2 (2.74%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
    461      45 (3.47%) 13 (1.63%) 28 (6.11%) 2 (0.99%)  3 (2.65%)  0 (0.00%)                                                                                                                                                                                                                                                                                                                                                                                                                                 
¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯¯ 

Past versions of unnamed-chunk-47-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

all clusters

               DAMs
GT_Treat        Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
  WT_Ctrl              417        283         18         89         17
  WT_Stroke            254        208         86         50         18
  APPPS1_Ctrl          389        141        189         32         47
  APPPS1_Stroke        238        167        165         32         31
               DAMs
GT_Treat        Microglia5
  WT_Ctrl                3
  WT_Stroke             38
  APPPS1_Ctrl           27
  APPPS1_Stroke          5

               DAMs
GT_Treat         Microglia0  Microglia1  Microglia2  Microglia3  Microglia4
  WT_Ctrl       0.504232164 0.342200726 0.021765417 0.107617896 0.020556227
  WT_Stroke     0.388379205 0.318042813 0.131498471 0.076452599 0.027522936
  APPPS1_Ctrl   0.471515152 0.170909091 0.229090909 0.038787879 0.056969697
  APPPS1_Stroke 0.373040752 0.261755486 0.258620690 0.050156740 0.048589342
               DAMs
GT_Treat         Microglia5
  WT_Ctrl       0.003627570
  WT_Stroke     0.058103976
  APPPS1_Ctrl   0.032727273
  APPPS1_Stroke 0.007836991

    Pearson's Chi-squared test

data:  restab
X-squared = 345.62, df = 15, p-value < 2.2e-16

Past versions of unnamed-chunk-49-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

      Dimension     Value Microglia0 Microglia1 Microglia2 Microglia3
1       WT_Ctrl Residuals   4.326069   5.399494 -12.519553  5.1749280
2       WT_Ctrl  p values   0.000364   0.000002   0.000000  0.0000050
3     WT_Stroke Residuals  -3.067114   3.041449  -1.925795  0.8581571
4     WT_Stroke  p values   0.051873   0.056506   1.000000  1.0000000
5   APPPS1_Ctrl Residuals   2.087847  -7.650778   6.867393 -4.0307171
6   APPPS1_Ctrl  p values   0.883480   0.000000   0.000000  0.0013350
7 APPPS1_Stroke Residuals  -3.900527  -0.618951   8.114322 -2.1172634
8 APPPS1_Stroke  p values   0.002304   1.000000   0.000000  0.8217000
  Microglia4 Microglia5
1  -3.146779  -4.616509
2   0.039619   0.000094
3  -1.639106   6.210771
4   1.000000   0.000000
5   3.275350   1.726722
6   0.025327   1.000000
7   1.516149  -3.112539
8   1.000000   0.044516

Past versions of unnamed-chunk-51-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Past versions of unnamed-chunk-53-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Comparison of DEGs in DAMs between treatments/genotypes

define DAM

DAM profiles based on Cell. 2017 Jun 15;169(7):1276-1290.e17. doi: 10.1016/j.cell.2017.05.018)

DAM1

Past versions of unnamed-chunk-54-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

       Clusters
DAMs     Microglia0  Microglia1  Microglia2  Microglia3  Microglia4  Microglia5
  FALSE 0.969183359 0.992490613 0.460698690 0.995073892 0.876106195 0.739726027
  TRUE  0.030816641 0.007509387 0.539301310 0.004926108 0.123893805 0.260273973

Past versions of unnamed-chunk-55-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

DAM2

Past versions of unnamed-chunk-56-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

       Clusters
DAM2     Microglia0  Microglia1  Microglia2  Microglia3  Microglia4  Microglia5
  FALSE 0.973035439 0.992490613 0.502183406 0.995073892 0.911504425 0.767123288
  TRUE  0.026964561 0.007509387 0.497816594 0.004926108 0.088495575 0.232876712

       DAMs
DAM2         FALSE       TRUE
  FALSE 0.98318686 0.22629969
  TRUE  0.01681314 0.77370031

Past versions of unnamed-chunk-57-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

               DAMs
GT_Treat        FALSE TRUE
  WT_Ctrl         827    0
  WT_Stroke       608   46
  APPPS1_Ctrl     653  172
  APPPS1_Stroke   529  109

               DAMs
GT_Treat             FALSE       TRUE
  WT_Ctrl       1.00000000 0.00000000
  WT_Stroke     0.92966361 0.07033639
  APPPS1_Ctrl   0.79151515 0.20848485
  APPPS1_Stroke 0.82915361 0.17084639

    Pearson's Chi-squared test

data:  restab
X-squared = 216.7, df = 3, p-value < 2.2e-16

      Dimension     Value      FALSE       TRUE
1       WT_Ctrl Residuals  11.987628 -11.987628
2       WT_Ctrl  p values   0.000000   0.000000
3     WT_Stroke Residuals   3.759161  -3.759161
4     WT_Stroke  p values   0.001364   0.001364
5   APPPS1_Ctrl Residuals -10.495487  10.495487
6   APPPS1_Ctrl  p values   0.000000   0.000000
7 APPPS1_Stroke Residuals  -5.428963   5.428963
8 APPPS1_Stroke  p values   0.000000   0.000000

DAMs in APPPS1 vs. DAMs in APPPS1 + Stroke

               DAMs
GT_Treat        FALSE TRUE
  APPPS1_Ctrl     653  172
  APPPS1_Stroke   529  109

               DAMs
GT_Treat            FALSE      TRUE
  APPPS1_Ctrl   0.7915152 0.2084848
  APPPS1_Stroke 0.8291536 0.1708464

    Fisher's Exact Test for Count Data

data:  restab
p-value = 0.07119
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.593415 1.028605
sample estimates:
odds ratio 
    0.7824 

Past versions of unnamed-chunk-59-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

DAMs in WT vs. DAMs in WT + Stroke

           DAMs
GT_Treat    FALSE TRUE
  WT_Ctrl     827    0
  WT_Stroke   608   46

           DAMs
GT_Treat         FALSE       TRUE
  WT_Ctrl   1.00000000 0.00000000
  WT_Stroke 0.92966361 0.07033639

    Fisher's Exact Test for Count Data

data:  restab
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 16.1857     Inf
sample estimates:
odds ratio 
       Inf 

Past versions of unnamed-chunk-60-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

DAM1 vs DAM2

               DAM2
GT_Treat        FALSE TRUE
  WT_Ctrl           0    0
  WT_Stroke        27   19
  APPPS1_Ctrl      13  159
  APPPS1_Stroke    34   75

               DAM2
GT_Treat            FALSE      TRUE
  WT_Ctrl                          
  WT_Stroke     0.5869565 0.4130435
  APPPS1_Ctrl   0.0755814 0.9244186
  APPPS1_Stroke 0.3119266 0.6880734

    Pearson's Chi-squared test

data:  restab
X-squared = NaN, df = 3, p-value = NA

      Dimension     Value     FALSE      TRUE
1       WT_Ctrl Residuals       NaN       NaN
2       WT_Ctrl  p values       NaN       NaN
3     WT_Stroke Residuals  6.306166 -6.306166
4     WT_Stroke  p values  0.000000  0.000000
5   APPPS1_Ctrl Residuals -6.861355  6.861355
6   APPPS1_Ctrl  p values  0.000000  0.000000
7 APPPS1_Stroke Residuals  2.616621 -2.616621
8 APPPS1_Stroke  p values  0.071044  0.071044

Past versions of unnamed-chunk-61-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

               DAM2
GT_Treat        FALSE TRUE
  APPPS1_Ctrl      13  159
  APPPS1_Stroke    34   75

               DAM2
GT_Treat            FALSE      TRUE
  APPPS1_Ctrl   0.0755814 0.9244186
  APPPS1_Stroke 0.3119266 0.6880734

    Pearson's Chi-squared test with Yates' continuity correction

data:  restab
X-squared = 25.087, df = 1, p-value = 5.479e-07

Past versions of unnamed-chunk-62-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

           DAM2
GT_Treat    FALSE TRUE
  WT_Stroke    27   19

           DAM2
GT_Treat        FALSE      TRUE
  WT_Stroke 0.5869565 0.4130435

    Chi-squared test for given probabilities

data:  restab
X-squared = 1.3913, df = 1, p-value = 0.2382

Past versions of unnamed-chunk-63-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Homeostatic Cells

Past versions of unnamed-chunk-64-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Past versions of unnamed-chunk-65-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

       Clusters
Homeo   Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
  FALSE  0.2681048  0.3504380  0.8515284  0.7241379  0.4513274  0.3835616
  TRUE   0.7318952  0.6495620  0.1484716  0.2758621  0.5486726  0.6164384

Past versions of unnamed-chunk-66-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Homeo vs DAM

Past versions of unnamed-chunk-67-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

               Homeo
GT_Treat        Neither Homeo DAM Unknown
  WT_Ctrl           213   614   0       0
  WT_Stroke         239   369  44       2
  APPPS1_Ctrl       203   450 164       8
  APPPS1_Stroke     277   252 104       5

               Homeo
GT_Treat            Neither       Homeo         DAM     Unknown
  WT_Ctrl       0.257557437 0.742442563 0.000000000 0.000000000
  WT_Stroke     0.365443425 0.564220183 0.067278287 0.003058104
  APPPS1_Ctrl   0.246060606 0.545454545 0.198787879 0.009696970
  APPPS1_Stroke 0.434169279 0.394984326 0.163009404 0.007836991

    Pearson's Chi-squared test

data:  restab
X-squared = 325.49, df = 9, p-value < 2.2e-16

      Dimension     Value   Neither       Homeo        DAM   Unknown
1       WT_Ctrl Residuals -4.302951  11.6592377 -11.676040 -2.426874
2       WT_Ctrl  p values  0.000270   0.0000000   0.000000  0.243673
3     WT_Stroke Residuals  3.046313  -0.4765131  -3.645594 -0.829592
4     WT_Stroke  p values  0.037067   1.0000000   0.004268  1.000000
5   APPPS1_Ctrl Residuals -5.132521  -1.8405306  10.208007  2.188247
6   APPPS1_Ctrl  p values  0.000005   1.0000000   0.000000  0.458426
7 APPPS1_Stroke Residuals  7.215188 -10.2316455   5.287851  1.099084
8 APPPS1_Stroke  p values  0.000000   0.0000000   0.000002  1.000000

Past versions of unnamed-chunk-68-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

            Homeo
Clust        Neither Homeo DAM Unknown
  Microglia0     310   948  38       2
  Microglia1     276   517   4       2
  Microglia2     150    61 240       7
  Microglia3     147    55   0       1
  Microglia4      38    61  13       1
  Microglia5      11    43  17       2

            Homeo
Clust            Neither       Homeo         DAM     Unknown
  Microglia0 0.238828968 0.730354391 0.029275809 0.001540832
  Microglia1 0.345431790 0.647058824 0.005006258 0.002503129
  Microglia2 0.327510917 0.133187773 0.524017467 0.015283843
  Microglia3 0.724137931 0.270935961 0.000000000 0.004926108
  Microglia4 0.336283186 0.539823009 0.115044248 0.008849558
  Microglia5 0.150684932 0.589041096 0.232876712 0.027397260

    Pearson's Chi-squared test

data:  restab
X-squared = 1349.2, df = 15, p-value < 2.2e-16

    Dimension     Value    Neither       Homeo         DAM     Unknown
1  Microglia0 Residuals -8.0536268  15.3880640 -12.0065476 -2.40533213
2  Microglia0  p values  0.0000000   0.0000000   0.0000000  0.38778700
3  Microglia1 Residuals  2.0543582   5.0006029 -10.8629350 -1.20557087
4  Microglia1  p values  0.9585850   0.0000140   0.0000000  1.00000000
5  Microglia2 Residuals  0.5474935 -20.6729086  31.6290145  3.33275814
6  Microglia2  p values  1.0000000   0.0000000   0.0000000  0.02063800
7  Microglia3 Residuals 12.9381381  -8.9960457  -5.0838972 -0.03504955
8  Microglia3  p values  0.0000000   0.0000000   0.0000090  1.00000000
9  Microglia4 Residuals  0.4592792  -0.7127124   0.3192794  0.57163244
10 Microglia4  p values  1.0000000   1.0000000   1.0000000  1.00000000
11 Microglia5 Residuals -3.0856938   0.2918834   3.5668728  2.71014789
12 Microglia5  p values  0.0487390   1.0000000   0.0086700  0.16140800

Past versions of unnamed-chunk-69-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

            Celltype
Clust        256#1022 256#1023 364#469 386 387 388 409 41738 41739 41799 42012
  Microglia0       59       55      69  12  11  52  56    60    55    77    33
  Microglia1       29       18      19   0   1  17   7    48    50    59    74
  Microglia2        3        2       3  17  10  53  27    32    56     4     8
  Microglia3       11       14       2   0   5   2   1    12     6     4    42
  Microglia4        3        4       4   4   1   8   4     8    10     3     3
  Microglia5        1        0       1   0   0  22   0     0     1    34     3
            Celltype
Clust        42013 42015 42042 42215 42217 42436 42438 42440 457 461
  Microglia0    67    99    76    46    89    91    69    88  89  45
  Microglia1    55    53    68    94    70    27    52    43   2  13
  Microglia2    39     4    30     5     1    38    23    20  55  28
  Microglia3     7     7     3    34    21     5    19     6   0   2
  Microglia4     9     1     4     2     3    15     8    14   2   3
  Microglia5     4     1     1     0     0     3     0     0   2   0

            Celltype
Clust           256#1022    256#1023     364#469         386         387
  Microglia0 0.045454545 0.042372881 0.053158706 0.009244992 0.008474576
  Microglia1 0.036295369 0.022528160 0.023779725 0.000000000 0.001251564
  Microglia2 0.006550218 0.004366812 0.006550218 0.037117904 0.021834061
  Microglia3 0.054187192 0.068965517 0.009852217 0.000000000 0.024630542
  Microglia4 0.026548673 0.035398230 0.035398230 0.035398230 0.008849558
  Microglia5 0.013698630 0.000000000 0.013698630 0.000000000 0.000000000
            Celltype
Clust                388         409       41738       41739       41799
  Microglia0 0.040061633 0.043143297 0.046224961 0.042372881 0.059322034
  Microglia1 0.021276596 0.008760951 0.060075094 0.062578223 0.073842303
  Microglia2 0.115720524 0.058951965 0.069868996 0.122270742 0.008733624
  Microglia3 0.009852217 0.004926108 0.059113300 0.029556650 0.019704433
  Microglia4 0.070796460 0.035398230 0.070796460 0.088495575 0.026548673
  Microglia5 0.301369863 0.000000000 0.000000000 0.013698630 0.465753425
            Celltype
Clust              42012       42013       42015       42042       42215
  Microglia0 0.025423729 0.051617874 0.076271186 0.058551618 0.035439137
  Microglia1 0.092615770 0.068836045 0.066332916 0.085106383 0.117647059
  Microglia2 0.017467249 0.085152838 0.008733624 0.065502183 0.010917031
  Microglia3 0.206896552 0.034482759 0.034482759 0.014778325 0.167487685
  Microglia4 0.026548673 0.079646018 0.008849558 0.035398230 0.017699115
  Microglia5 0.041095890 0.054794521 0.013698630 0.013698630 0.000000000
            Celltype
Clust              42217       42436       42438       42440         457
  Microglia0 0.068567026 0.070107858 0.053158706 0.067796610 0.068567026
  Microglia1 0.087609512 0.033792240 0.065081352 0.053817272 0.002503129
  Microglia2 0.002183406 0.082969432 0.050218341 0.043668122 0.120087336
  Microglia3 0.103448276 0.024630542 0.093596059 0.029556650 0.000000000
  Microglia4 0.026548673 0.132743363 0.070796460 0.123893805 0.017699115
  Microglia5 0.000000000 0.041095890 0.000000000 0.000000000 0.027397260
            Celltype
Clust                461
  Microglia0 0.034668721
  Microglia1 0.016270338
  Microglia2 0.061135371
  Microglia3 0.009852217
  Microglia4 0.026548673
  Microglia5 0.000000000

    Pearson's Chi-squared test

data:  restab
X-squared = 1161.7, df = 100, p-value < 2.2e-16

    Dimension     Value    256#1022   256#1023    364#469        386
1  Microglia0 Residuals  2.44377348  2.9705510  5.3371695 -0.8989740
2  Microglia0  p values  1.00000000  0.3745550  0.0000120  1.0000000
3  Microglia1 Residuals  0.05153557 -1.7156438 -1.7552529 -3.5258555
4  Microglia1  p values  1.00000000  1.0000000  1.0000000  0.0531870
5  Microglia2 Residuals -3.68206945 -3.6247877 -3.4712387  5.7313357
6  Microglia2  p values  0.02915000  0.0364390  0.0652760  0.0000010
7  Microglia3 Residuals  1.44104299  3.1553761 -1.9290790 -1.5721655
8  Microglia3  p values  1.00000000  0.2019670  1.0000000  1.0000000
9  Microglia4 Residuals -0.55024909  0.2360458  0.1275165  2.4906670
10 Microglia4  p values  1.00000000  1.0000000  1.0000000  1.0000000
11 Microglia5 Residuals -1.03592849 -1.5626316 -0.9448057 -0.9211908
12 Microglia5  p values  1.00000000  1.0000000  1.0000000  1.0000000
           387        388        409      41738      41739      41799
1  -0.51444512 -2.6505570  2.9649778 -1.7264092 -3.6568691 -0.4330528
2   1.00000000  1.0000000  0.3814080  1.0000000  0.0321700  1.0000000
3  -2.81797531 -4.6156234 -4.4052992  0.8366028  0.2940361  1.7041261
4   0.60892700  0.0004940  0.0013310  1.0000000  1.0000000  1.0000000
5   2.95691820  6.6326832  3.5165321  1.5944787  6.0395281 -5.1139895
6   0.39152000  0.0000000  0.0550900  1.0000000  0.0000000  0.0000400
7   2.30022232 -2.8157419 -2.2847410  0.3103929 -1.9146843 -2.5680472
8   1.00000000  0.6131760  1.0000000  1.0000000  1.0000000  1.0000000
9  -0.07386006  0.9000619  0.1919563  0.7865226  1.2750261 -1.5764257
10  1.00000000  1.0000000  1.0000000  1.0000000  1.0000000  1.0000000
11 -0.84781089  9.6781691 -1.5798990 -2.0741450 -1.6975433 14.5611594
12  1.00000000  0.0000000  1.0000000  1.0000000  1.0000000  0.0000000
        42012      42013     42015      42042     42215     42217     42436
1  -6.3085838 -1.9783952  4.236734 -0.6540351 -5.223614  1.207651  1.876414
2   0.0000000  1.0000000  0.002858  1.0000000  0.000022  1.000000  1.000000
3   5.3936885  1.0139659  1.481007  3.2019076  7.743028  3.435115 -3.742891
4   0.0000090  1.0000000  1.000000  0.1720160  0.000000  0.074630  0.022921
5  -3.8594836  2.2950468 -4.790482  0.3560163 -4.902303 -5.803129  2.160416
6   0.0143170  1.0000000  0.000210  1.0000000  0.000119  0.000001  1.000000
7   9.7837126 -1.6596083 -1.384306 -2.8843069  6.516341  2.497885 -2.235052
8   0.0000000  1.0000000  1.000000  0.4942680  0.000000  1.000000  1.000000
9  -1.3659921  0.8197522 -2.224338 -1.1893265 -1.975789 -1.610006  3.263494
10  1.0000000  1.0000000  1.000000  1.0000000  1.000000  1.000000  0.138660
11 -0.5398963 -0.2408341 -1.592919 -1.7288124 -2.214433 -2.233923 -0.713461
12  1.0000000  1.0000000  1.000000  1.0000000  1.000000  1.000000  1.000000
        42438      42440        457        461
1  -1.0146340  2.0006974  3.8599005  1.0463090
2   1.0000000  1.0000000  0.0142930  1.0000000
3   0.9906319 -0.6041055 -7.2959710 -2.8011450
4   1.0000000  1.0000000  0.0000000  0.6416130
5  -0.7831848 -1.4353711  7.3221036  4.0670945
6   1.0000000  1.0000000  0.0000000  0.0059980
7   2.2418170 -1.8009111 -3.4213290 -1.7965860
8   1.0000000  1.0000000  0.0785180  1.0000000
9   0.5891480  3.0499452 -1.6392099 -0.2731842
10  1.0000000  0.2883930  1.0000000  1.0000000
11 -2.1485074 -2.1485074 -0.9267321 -1.5451959
12  1.0000000  1.0000000  1.0000000  1.0000000

Past versions of unnamed-chunk-70-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

      Clust
gender Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
     f        444        251        124         27         35          7
     m        854        548        334        176         78         66

      Clust
gender  Microglia0  Microglia1  Microglia2  Microglia3  Microglia4  Microglia5
     f 0.500000000 0.282657658 0.139639640 0.030405405 0.039414414 0.007882883
     m 0.415369650 0.266536965 0.162451362 0.085603113 0.037937743 0.032101167

    Pearson's Chi-squared test

data:  restab
X-squared = 54.849, df = 5, p-value = 1.402e-10

  Dimension     Value Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
1         f Residuals   4.244835  0.9027835  -1.567335  -5.425071  0.1914087
2         f  p values   0.000263  1.0000000   1.000000   0.000001  1.0000000
3         m Residuals  -4.244835 -0.9027835   1.567335   5.425071 -0.1914087
4         m  p values   0.000263  1.0000000   1.000000   0.000001  1.0000000
  Microglia5
1  -3.878397
2   0.001262
3   3.878397
4   0.001262

Past versions of unnamed-chunk-71-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Past versions of unnamed-chunk-72-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Homeo in Genotype Treatment

proportion tables show percentages of Homeostatic cells per condition

               Homeo
GT_Treat        FALSE TRUE
  WT_Ctrl         213  614
  WT_Stroke       283  371
  APPPS1_Ctrl     367  458
  APPPS1_Stroke   381  257

               Homeo
GT_Treat            FALSE      TRUE
  WT_Ctrl       0.2575574 0.7424426
  WT_Stroke     0.4327217 0.5672783
  APPPS1_Ctrl   0.4448485 0.5551515
  APPPS1_Stroke 0.5971787 0.4028213

    Pearson's Chi-squared test

data:  restab
X-squared = 173.96, df = 3, p-value < 2.2e-16

      Dimension     Value       FALSE        TRUE
1       WT_Ctrl Residuals -11.3276598  11.3276598
2       WT_Ctrl  p values   0.0000000   0.0000000
3     WT_Stroke Residuals   0.5968313  -0.5968313
4     WT_Stroke  p values   1.0000000   1.0000000
5   APPPS1_Ctrl Residuals   1.5280030  -1.5280030
6   APPPS1_Ctrl  p values   1.0000000   1.0000000
7 APPPS1_Stroke Residuals  10.0892181 -10.0892181
8 APPPS1_Stroke  p values   0.0000000   0.0000000

Past versions of unnamed-chunk-73-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

               Homeo
GT_Treat        FALSE TRUE
  APPPS1_Ctrl     367  458
  APPPS1_Stroke   381  257

               Homeo
GT_Treat            FALSE      TRUE
  APPPS1_Ctrl   0.4448485 0.5551515
  APPPS1_Stroke 0.5971787 0.4028213

    Pearson's Chi-squared test with Yates' continuity correction

data:  restab
X-squared = 32.804, df = 1, p-value = 1.02e-08

Past versions of unnamed-chunk-74-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

           Homeo
GT_Treat    FALSE TRUE
  WT_Ctrl     213  614
  WT_Stroke   283  371

           Homeo
GT_Treat        FALSE      TRUE
  WT_Ctrl   0.2575574 0.7424426
  WT_Stroke 0.4327217 0.5672783

    Pearson's Chi-squared test with Yates' continuity correction

data:  restab
X-squared = 49.522, df = 1, p-value = 1.962e-12

Past versions of unnamed-chunk-75-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Spatial cell types

Past versions of unnamed-chunk-76-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Distal Cell types

Past versions of unnamed-chunk-77-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

       Clusters
Distals Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
  FALSE  0.7688752  0.6958698  0.3864629  0.8029557  0.6548673  0.6301370
  TRUE   0.2311248  0.3041302  0.6135371  0.1970443  0.3451327  0.3698630

Control Cell types

Past versions of unnamed-chunk-78-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

        Clusters
Controls Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
   FALSE  0.4522342  0.4856070  0.5567686  0.5714286  0.5309735  0.5342466
   TRUE   0.5477658  0.5143930  0.4432314  0.4285714  0.4690265  0.4657534

#### Peri_ictus Cell types

Past versions of unnamed-chunk-79-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

       Clusters
Strokes Microglia0 Microglia1 Microglia2 Microglia3 Microglia4 Microglia5
  FALSE 0.93220339 0.95994994 0.40611354 0.98029557 0.80530973 0.71232877
  TRUE  0.06779661 0.04005006 0.59388646 0.01970443 0.19469027 0.28767123

Past versions of unnamed-chunk-80-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

proportion tables show percebtages of DAM cells per condition

Distals binary proportions

               Distals
GT_Treat        FALSE TRUE
  WT_Ctrl         641  186
  WT_Stroke       496  158
  APPPS1_Ctrl     494  331
  APPPS1_Stroke   383  255

               Distals
GT_Treat            FALSE      TRUE
  WT_Ctrl       0.7750907 0.2249093
  WT_Stroke     0.7584098 0.2415902
  APPPS1_Ctrl   0.5987879 0.4012121
  APPPS1_Stroke 0.6003135 0.3996865

    Pearson's Chi-squared test

data:  restab
X-squared = 96.905, df = 3, p-value < 2.2e-16

Past versions of unnamed-chunk-81-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

      Dimension     Value     FALSE      TRUE
1       WT_Ctrl Residuals  6.637572 -6.637572
2       WT_Ctrl  p values  0.000000  0.000000
3     WT_Stroke Residuals  4.634828 -4.634828
4     WT_Stroke  p values  0.000029  0.000029
5   APPPS1_Ctrl Residuals -6.213329  6.213329
6   APPPS1_Ctrl  p values  0.000000  0.000000
7 APPPS1_Stroke Residuals -5.144074  5.144074
8 APPPS1_Stroke  p values  0.000002  0.000002

Distals in APPPS1

               Distals
GT_Treat        FALSE TRUE
  APPPS1_Ctrl     494  331
  APPPS1_Stroke   383  255

               Distals
GT_Treat            FALSE      TRUE
  APPPS1_Ctrl   0.5987879 0.4012121
  APPPS1_Stroke 0.6003135 0.3996865

    Fisher's Exact Test for Count Data

data:  restab
p-value = 0.9572
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.8000638 1.2337160
sample estimates:
odds ratio 
 0.9936697 

Past versions of unnamed-chunk-82-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Distals in WT

           Distals
GT_Treat    FALSE TRUE
  WT_Ctrl     641  186
  WT_Stroke   496  158

           Distals
GT_Treat        FALSE      TRUE
  WT_Ctrl   0.7750907 0.2249093
  WT_Stroke 0.7584098 0.2415902

    Fisher's Exact Test for Count Data

data:  restab
p-value = 0.4577
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.8547616 1.4087562
sample estimates:
odds ratio 
  1.097723 

Past versions of unnamed-chunk-83-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Controls binary proportions

               Controls
GT_Treat        FALSE TRUE
  WT_Ctrl         324  503
  WT_Stroke       321  333
  APPPS1_Ctrl     455  370
  APPPS1_Stroke   345  293

               Controls
GT_Treat            FALSE      TRUE
  WT_Ctrl       0.3917775 0.6082225
  WT_Stroke     0.4908257 0.5091743
  APPPS1_Ctrl   0.5515152 0.4484848
  APPPS1_Stroke 0.5407524 0.4592476

    Pearson's Chi-squared test

data:  restab
X-squared = 50.986, df = 3, p-value = 4.925e-11

Past versions of unnamed-chunk-84-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

      Dimension     Value         FALSE          TRUE
1       WT_Ctrl Residuals -6.7193065248  6.7193065248
2       WT_Ctrl  p values  0.0000000000  0.0000000000
3     WT_Stroke Residuals -0.0001807502  0.0001807502
4     WT_Stroke  p values  1.0000000000  1.0000000000
5   APPPS1_Ctrl Residuals  4.1098357128 -4.1098357128
6   APPPS1_Ctrl  p values  0.0003170000  0.0003170000
7 APPPS1_Stroke Residuals  2.8500868085 -2.8500868085
8 APPPS1_Stroke  p values  0.0349660000  0.0349660000

Controls in APPPS1

               Controls
GT_Treat        FALSE TRUE
  APPPS1_Ctrl     455  370
  APPPS1_Stroke   345  293

               Controls
GT_Treat            FALSE      TRUE
  APPPS1_Ctrl   0.5515152 0.4484848
  APPPS1_Stroke 0.5407524 0.4592476

    Fisher's Exact Test for Count Data

data:  restab
p-value = 0.7109
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.8439753 1.2922035
sample estimates:
odds ratio 
  1.044378 

Past versions of unnamed-chunk-85-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Controls in WT

           Controls
GT_Treat    FALSE TRUE
  WT_Ctrl     324  503
  WT_Stroke   321  333

           Controls
GT_Treat        FALSE      TRUE
  WT_Ctrl   0.3917775 0.6082225
  WT_Stroke 0.4908257 0.5091743

    Fisher's Exact Test for Count Data

data:  restab
p-value = 0.0001448
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.5401406 0.8267237
sample estimates:
odds ratio 
 0.6684173 

Past versions of unnamed-chunk-86-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Peri_ictus binary proportions

               Peri_Ictal
GT_Treat        FALSE TRUE
  WT_Ctrl         825    2
  WT_Stroke       562   92
  APPPS1_Ctrl     637  188
  APPPS1_Stroke   481  157

               Peri_Ictal
GT_Treat             FALSE       TRUE
  WT_Ctrl       0.99758162 0.00241838
  WT_Stroke     0.85932722 0.14067278
  APPPS1_Ctrl   0.77212121 0.22787879
  APPPS1_Stroke 0.75391850 0.24608150

    Pearson's Chi-squared test

data:  restab
X-squared = 228.25, df = 3, p-value < 2.2e-16

Past versions of unnamed-chunk-87-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

      Dimension     Value      FALSE        TRUE
1       WT_Ctrl Residuals 13.9665290 -13.9665290
2       WT_Ctrl  p values  0.0000000   0.0000000
3     WT_Stroke Residuals  0.6873743  -0.6873743
4     WT_Stroke  p values  1.0000000   1.0000000
5   APPPS1_Ctrl Residuals -7.4859769   7.4859769
6   APPPS1_Ctrl  p values  0.0000000   0.0000000
7 APPPS1_Stroke Residuals -7.7689931   7.7689931
8 APPPS1_Stroke  p values  0.0000000   0.0000000

Peri_ictus in APPPS1

               Peri_Ictal
GT_Treat        FALSE TRUE
  APPPS1_Ctrl     637  188
  APPPS1_Stroke   481  157

               Peri_Ictal
GT_Treat            FALSE      TRUE
  APPPS1_Ctrl   0.7721212 0.2278788
  APPPS1_Stroke 0.7539185 0.2460815

    Fisher's Exact Test for Count Data

data:  restab
p-value = 0.4202
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
 0.8606895 1.4198329
sample estimates:
odds ratio 
  1.105874 

Past versions of unnamed-chunk-88-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Peri_ictus WT

           Peri_Ictal
GT_Treat    FALSE TRUE
  WT_Ctrl     825    2
  WT_Stroke   562   92

           Peri_Ictal
GT_Treat         FALSE       TRUE
  WT_Ctrl   0.99758162 0.00241838
  WT_Stroke 0.85932722 0.14067278

    Fisher's Exact Test for Count Data

data:  restab
p-value < 2.2e-16
alternative hypothesis: true odds ratio is not equal to 1
95 percent confidence interval:
  18.00707 566.38843
sample estimates:
odds ratio 
  67.33587 

Past versions of unnamed-chunk-89-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

DEG comparing conditions overall

WT Stroke vs no Stroke

avg_logFC: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group

Past versions of unnamed-chunk-90-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

character(0)

APPPS1 Stroke vs APPPS1 no Stroke

avg_logFC: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group

[1] "AC121793.2" "Olfr907"    "S100a6"    

WT Stroke vs APPPS1Stroke

[1] "Lilrb4"

WT ctr; vs APPPS1 ctrl

avg_logFC: log fold-chage of the average expression between the two groups. Positive values indicate that the gene is more highly expressed in the first group

[1] "Olfr633"  "Olfr1178"

Scatterplot of DEGs of all four conditions

see https://www.nature.com/articles/s41593-023-01355-y ; see Fig 1e

[1] "S100a6 cannot be found"

[1] "S100a6 cannot be found" "Atp1a2 cannot be found" "Fn1 cannot be found"   
[4] "Ntrk2 cannot be found" 

Past versions of unnamed-chunk-99-2.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

DEG Stroke Cells only

DEG comparing Cluster

All Clusters versus All Clusters

Define Main analysis pipeline

DEG run for each combination

[1] "Microglia0_vs_Microglia1"
[1] "all"

[1] "comorbid"

[1] "Microglia0_vs_Microglia2"
[1] "all"

[1] "comorbid"

[1] "Microglia0_vs_Microglia3"
[1] "all"

[1] "comorbid"

[1] "Microglia0_vs_Microglia4"
[1] "all"

[1] "comorbid"

[1] "Microglia0_vs_Microglia5"
[1] "all"

[1] "comorbid"

[1] "Microglia1_vs_Microglia2"
[1] "all"

[1] "comorbid"

[1] "Microglia1_vs_Microglia3"
[1] "all"

[1] "comorbid"

[1] "Microglia1_vs_Microglia4"
[1] "all"

[1] "comorbid"

[1] "Microglia1_vs_Microglia5"
[1] "all"

[1] "comorbid"

[1] "Microglia2_vs_Microglia3"
[1] "all"

[1] "comorbid"

[1] "Microglia2_vs_Microglia4"
[1] "all"

[1] "comorbid"

[1] "Microglia2_vs_Microglia5"
[1] "all"

[1] "comorbid"

[1] "Microglia3_vs_Microglia4"
[1] "all"

[1] "comorbid"

[1] "Microglia3_vs_Microglia5"
[1] "all"

[1] "comorbid"

[1] "Microglia4_vs_Microglia5"
[1] "all"

[1] "comorbid"

Microglia0_vs_Microglia1

Past versions of unnamed-chunk-103-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-2.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Trac	0	-1.7063491	0.660	0.869	0
Arfgef3	0	-1.0887626	0.665	0.874	0
Vmn1r218	0	0.8801728	0.898	0.717	0
Cpa6	0	1.3559398	0.760	0.522	0
Lipe	0	-1.1115953	0.851	0.935	0
Or4f14b	0	0.9868262	0.956	0.832	0
Or51q1	0	0.8486383	0.922	0.778	0
Vmn1r201	0	1.8546872	0.588	0.344	0
Fgd4	0	0.4592167	0.933	0.805	0
Vmn1r76	0	1.3102043	0.810	0.615	0
Or13a17	0	0.5632069	0.797	0.593	0
Vmn1r81	0	1.0998458	0.935	0.791	0
Or1f19	0	1.1797206	0.800	0.603	0
Vmn1r6	0	1.0752258	0.739	0.533	0
Or6z3	0	0.8587296	0.901	0.741	0
Psg16	0	0.8487776	0.820	0.605	0
Cyb5r4	0	0.8345815	0.733	0.529	0
Nipal2	0	0.7547669	0.817	0.630	0
Or13a18	0	0.7794006	0.844	0.701	0
Slc38a6	0	0.6364006	0.893	0.718	0
Sik2	0	0.5163416	0.878	0.708	0
Or13a25	0	0.8214713	0.767	0.552	0
Traf5	0	0.3551980	0.794	0.608	0
Snhg14	0	1.0264191	0.911	0.762	0
Or6c6c	0	0.6616574	0.723	0.507	0
Zfp369	0	0.4648512	0.871	0.666	0
Sros1	0	0.8076862	0.812	0.646	0
Vmn1r197	0	1.2872492	0.785	0.611	0
Cep112it	0	1.0929949	0.611	0.395	0
Or6c8	0	1.5051352	0.669	0.462	0
Cux2	0	-0.9025422	0.808	0.924	0
Prdm11	0	0.4472788	0.614	0.385	0
Acad9	0	0.4533341	0.787	0.612	0
Hsd3b2	0	1.9297267	0.635	0.442	0
Cul4a	0	0.7300919	0.729	0.547	0
Slfn3	0	0.5367422	0.700	0.483	0
Eif2a	0	-0.7878757	0.865	0.937	0
Or10ag54	0	0.8337652	0.820	0.650	0
Vmn1r46	0	0.8794171	0.794	0.602	0
Or10h28	0	0.7131371	0.790	0.615	0
Nopchap1	0	0.8011462	0.986	0.934	0
Vmn1r18	0	1.1206616	0.776	0.596	0
Or52k2	0	0.8714795	0.703	0.523	0
Or1ab2	0	0.9178200	0.773	0.586	0
Maip1	0	0.5767887	0.650	0.447	0
Or4a77	0	1.4103791	0.671	0.458	0
Or1j15	0	0.9185293	0.849	0.723	0
Or51k1	0	1.1480351	0.812	0.667	0
Vmn1r58	0	0.8989285	0.767	0.576	0
Pax6	0	-0.9621078	0.720	0.846	0
Tmcc1	0	0.3037596	0.914	0.797	0
Or4c115	0	1.3483142	0.591	0.390	0
Bltp1	0	0.5276250	0.713	0.506	0
Grip2	0	1.4998994	0.881	0.777	0
Senp7	0	0.3728211	0.830	0.671	0
Grk4	0	0.6580214	0.807	0.642	0
Lars2	0	-0.2339387	0.833	0.682	0
Ucp2	0	0.7092400	0.421	0.210	0
Kcnq1ot1	0	0.4429731	0.971	0.907	0
Or6c208	0	1.0712086	0.675	0.479	0
Or52m1	0	-1.4214082	0.659	0.807	0
9930111J21Rik2	0	0.2874189	0.918	0.768	0
Or7g23	0	0.7463336	0.740	0.591	0
Ranbp3l	0	0.8859967	0.735	0.532	0
Cep290	0	-0.9642513	0.828	0.916	0
Ccdc82	0	0.7570261	0.717	0.542	0
St14	0	0.6868633	0.671	0.471	0
Nox4	0	0.4297913	0.600	0.370	0
Ift20	0	-0.7147168	0.729	0.872	0
Zfp65	0	0.5765027	0.545	0.349	0
Lpl	0	0.3464301	0.739	0.541	0
Rrm1	0	0.2793334	0.721	0.543	0
Or5b124	0	0.9798651	0.686	0.534	0
Nom1	0	0.7170819	0.793	0.617	0
Bora	0	0.5744559	0.504	0.307	0
Pign	0	0.4839414	0.810	0.631	0
Vmn1r72	0	0.7085967	0.716	0.537	0
Dpf1	0	-0.7708053	0.531	0.682	0
Macrod2os1	0	0.8181883	0.522	0.327	0
Pi15	0	0.9551680	0.636	0.442	0
Cflar	0	0.1832956	0.827	0.677	0
Glrx2	0	0.3575157	0.751	0.572	0
Ncf2	0	0.3230060	0.720	0.523	0
Zfp738	0	0.4564973	0.831	0.667	0
Cnpy3	0	0.6840410	0.550	0.347	0
Or4p4	0	0.9283994	0.733	0.548	0
mt-Tq	0	-1.4433784	0.689	0.805	0
Syndig1l	0	-0.5406834	0.559	0.726	0
Zkscan3	0	0.0640989	0.697	0.488	0
Vmn1r209	0	1.3133292	0.552	0.364	0
Fchsd2	0	0.1316013	0.752	0.534	0
Vmn1r87	0	0.6492669	0.775	0.605	0
Foxp2	0	0.7990055	0.607	0.434	0
Eif2ak2	0	-0.3034954	0.696	0.494	0
Or1l4	0	0.6202373	0.690	0.518	0
Or52e19	0	1.4995549	0.401	0.217	0
Mrpl48	0	-0.1820045	0.683	0.497	0
Pkib	0	0.2775215	0.786	0.599	0
Haus8	0	0.4061894	0.757	0.594	0
Zfp729a	0	0.0280478	0.574	0.375	0

Microglia0_vs_Microglia1_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-5.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Trac	0	-1.7063491	0.660	0.869	0
Arfgef3	0	-1.0887626	0.665	0.874	0
Vmn1r218	0	0.8801728	0.898	0.717	0
Cpa6	0	1.3559398	0.760	0.522	0
Lipe	0	-1.1115953	0.851	0.935	0
Or4f14b	0	0.9868262	0.956	0.832	0
Or51q1	0	0.8486383	0.922	0.778	0
Vmn1r201	0	1.8546872	0.588	0.344	0
Fgd4	0	0.4592167	0.933	0.805	0
Vmn1r76	0	1.3102043	0.810	0.615	0
Or13a17	0	0.5632069	0.797	0.593	0
Vmn1r81	0	1.0998458	0.935	0.791	0
Or1f19	0	1.1797206	0.800	0.603	0
Vmn1r6	0	1.0752258	0.739	0.533	0
Or6z3	0	0.8587296	0.901	0.741	0
Psg16	0	0.8487776	0.820	0.605	0
Cyb5r4	0	0.8345815	0.733	0.529	0
Nipal2	0	0.7547669	0.817	0.630	0
Or13a18	0	0.7794006	0.844	0.701	0
Slc38a6	0	0.6364006	0.893	0.718	0
Sik2	0	0.5163416	0.878	0.708	0
Or13a25	0	0.8214713	0.767	0.552	0
Traf5	0	0.3551980	0.794	0.608	0
Snhg14	0	1.0264191	0.911	0.762	0
Or6c6c	0	0.6616574	0.723	0.507	0
Zfp369	0	0.4648512	0.871	0.666	0
Sros1	0	0.8076862	0.812	0.646	0
Vmn1r197	0	1.2872492	0.785	0.611	0
Cep112it	0	1.0929949	0.611	0.395	0
Or6c8	0	1.5051352	0.669	0.462	0
Cux2	0	-0.9025422	0.808	0.924	0
Prdm11	0	0.4472788	0.614	0.385	0
Acad9	0	0.4533341	0.787	0.612	0
Hsd3b2	0	1.9297267	0.635	0.442	0
Cul4a	0	0.7300919	0.729	0.547	0
Slfn3	0	0.5367422	0.700	0.483	0
Eif2a	0	-0.7878757	0.865	0.937	0
Or10ag54	0	0.8337652	0.820	0.650	0
Vmn1r46	0	0.8794171	0.794	0.602	0
Or10h28	0	0.7131371	0.790	0.615	0
Nopchap1	0	0.8011462	0.986	0.934	0
Vmn1r18	0	1.1206616	0.776	0.596	0
Or52k2	0	0.8714795	0.703	0.523	0
Or1ab2	0	0.9178200	0.773	0.586	0
Maip1	0	0.5767887	0.650	0.447	0
Or4a77	0	1.4103791	0.671	0.458	0
Or1j15	0	0.9185293	0.849	0.723	0
Or51k1	0	1.1480351	0.812	0.667	0
Vmn1r58	0	0.8989285	0.767	0.576	0
Pax6	0	-0.9621078	0.720	0.846	0
Tmcc1	0	0.3037596	0.914	0.797	0
Or4c115	0	1.3483142	0.591	0.390	0
Bltp1	0	0.5276250	0.713	0.506	0
Grip2	0	1.4998994	0.881	0.777	0
Senp7	0	0.3728211	0.830	0.671	0
Grk4	0	0.6580214	0.807	0.642	0
Lars2	0	-0.2339387	0.833	0.682	0
Ucp2	0	0.7092400	0.421	0.210	0
Kcnq1ot1	0	0.4429731	0.971	0.907	0
Or6c208	0	1.0712086	0.675	0.479	0
Or52m1	0	-1.4214082	0.659	0.807	0
9930111J21Rik2	0	0.2874189	0.918	0.768	0
Or7g23	0	0.7463336	0.740	0.591	0
Ranbp3l	0	0.8859967	0.735	0.532	0
Cep290	0	-0.9642513	0.828	0.916	0
Ccdc82	0	0.7570261	0.717	0.542	0
St14	0	0.6868633	0.671	0.471	0
Nox4	0	0.4297913	0.600	0.370	0
Ift20	0	-0.7147168	0.729	0.872	0
Zfp65	0	0.5765027	0.545	0.349	0
Lpl	0	0.3464301	0.739	0.541	0
Rrm1	0	0.2793334	0.721	0.543	0
Or5b124	0	0.9798651	0.686	0.534	0
Nom1	0	0.7170819	0.793	0.617	0
Bora	0	0.5744559	0.504	0.307	0
Pign	0	0.4839414	0.810	0.631	0
Vmn1r72	0	0.7085967	0.716	0.537	0
Dpf1	0	-0.7708053	0.531	0.682	0
Macrod2os1	0	0.8181883	0.522	0.327	0
Pi15	0	0.9551680	0.636	0.442	0
Cflar	0	0.1832956	0.827	0.677	0
Glrx2	0	0.3575157	0.751	0.572	0
Ncf2	0	0.3230060	0.720	0.523	0
Zfp738	0	0.4564973	0.831	0.667	0
Cnpy3	0	0.6840410	0.550	0.347	0
Or4p4	0	0.9283994	0.733	0.548	0
mt-Tq	0	-1.4433784	0.689	0.805	0
Syndig1l	0	-0.5406834	0.559	0.726	0
Zkscan3	0	0.0640989	0.697	0.488	0
Vmn1r209	0	1.3133292	0.552	0.364	0
Fchsd2	0	0.1316013	0.752	0.534	0
Vmn1r87	0	0.6492669	0.775	0.605	0
Foxp2	0	0.7990055	0.607	0.434	0
Eif2ak2	0	-0.3034954	0.696	0.494	0
Or1l4	0	0.6202373	0.690	0.518	0
Or52e19	0	1.4995549	0.401	0.217	0
Mrpl48	0	-0.1820045	0.683	0.497	0
Pkib	0	0.2775215	0.786	0.599	0
Haus8	0	0.4061894	0.757	0.594	0
Zfp729a	0	0.0280478	0.574	0.375	0

Microglia0_vs_Microglia2

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-8.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Cst7	0	-3.9686104	0.141	0.705	0
Apoe	0	-2.6506012	0.616	0.937	0
Clec7a	0	-2.8912634	0.138	0.668	0
Ccl3	0	-4.3531509	0.093	0.533	0
Lyz2	0	-1.9620885	0.636	0.921	0
Ctsb	0	-1.2553728	0.965	0.993	0
P2ry12	0	1.3417683	0.976	0.915	0
Axl	0	-2.6048608	0.106	0.533	0
Fth1	0	-1.1728108	0.952	0.983	0
Ctsz	0	-1.1364535	0.951	0.987	0
Ftl1	0	-1.0845956	0.948	0.976	0
B2m	0	-0.8841796	0.984	0.989	0
Ccl4	0	-5.4590391	0.041	0.332	0
Tmem119	0	1.3086498	0.951	0.760	0
Cd63	0	-1.5218787	0.675	0.893	0
Ctsd	0	-1.0327399	0.996	1.000	0
Lilrb4a	0	-4.0914589	0.050	0.345	0
Selplg	0	0.9323382	0.982	0.924	0
Baiap2l2	0	-3.2808146	0.015	0.238	0
Serinc3	0	0.7581640	0.984	0.976	0
Eef1a1	0	-0.9604677	0.946	0.989	0
Cox6a2	0	-3.6852880	0.034	0.282	0
Cd9	0	-1.0278271	0.918	0.969	0
Mif	0	-1.8511946	0.237	0.605	0
Tyrobp	0	-1.2701819	0.950	0.980	0
Npc2	0	-1.1582156	0.805	0.926	0
Rpl41	0	-1.2166273	0.773	0.930	0
Ank	0	-2.5357887	0.150	0.467	0
Cx3cr1	0	0.8703880	0.992	0.972	0
Lgals3bp	0	-1.5832710	0.433	0.758	0
Capg	0	-2.4097202	0.103	0.406	0
Itgax	0	-3.3825661	0.045	0.286	0
Malat1	0	0.5418416	0.992	0.952	0
Cd74	0	-2.4327293	0.130	0.443	0
Rpl18a	0	-0.9815482	0.873	0.952	0
Csf1	0	-2.9261667	0.052	0.301	0
Myo1e	0	-2.4967895	0.082	0.358	0
Cd52	0	-1.5075890	0.426	0.738	0
Cd68	0	-1.0343826	0.820	0.932	0
Rpl35rt	0	-1.1885764	0.731	0.915	0
Ccl6	0	-2.4365684	0.277	0.587	0
Ch25h	0	-4.4413136	0.015	0.201	0
Ctsl	0	-1.0159982	0.924	0.969	0
Ivns1abp	0	1.2930563	0.888	0.731	0
Gnas	0	-1.6204026	0.442	0.734	0
Ctss	0	-0.4719540	0.995	1.000	0
Hif1a	0	-1.5643552	0.262	0.587	0
Rplp1	0	-0.9466536	0.802	0.932	0
Gapdh	0	-1.2885205	0.661	0.841	0
Spp1	0	-7.7962458	0.017	0.177	0
Rpl21	0	-1.1188142	0.636	0.856	0
Rps28	0	-1.0568365	0.701	0.891	0
H2-D1	0	-0.8545038	0.831	0.941	0
Aldoa	0	-1.2316458	0.545	0.784	0
Rpl35	0	-1.0361363	0.760	0.928	0
Rpl32	0	-0.9739009	0.670	0.882	0
Rps18	0	-1.0264550	0.681	0.865	0
Ramp1	0	-2.0014110	0.123	0.380	0
Serpine2	0	-1.0954029	0.844	0.928	0
Uba52	0	-1.0300158	0.559	0.812	0
Anxa5	0	-1.9086755	0.131	0.389	0
Cpd	0	-1.7734823	0.094	0.328	0
Crlf2	0	-1.6833915	0.099	0.338	0
Nicol1	0	-2.8912067	0.022	0.179	0
Tpi1	0	-1.5549716	0.174	0.441	0
Rps16-ps2	0	-1.2757444	0.430	0.701	0
Mt1	0	-1.1482896	0.276	0.594	0
Wfdc17	0	-3.4174334	0.010	0.140	0
Ifi27l2a	0	-1.4590027	0.137	0.393	0
Lpl	0	-3.0948877	0.739	0.825	0
Rpl37a	0	-0.9054676	0.697	0.865	0
Maf	0	1.1640231	0.856	0.688	0
Zfp691	0	1.3945194	0.872	0.758	0
Tpt1	0	-1.1415396	0.618	0.825	0
Rps19	0	-0.9052618	0.703	0.871	0
Plaur	0	-2.6550672	0.085	0.290	0
Csf1r	0	0.4878526	0.991	0.991	0
Rpl10a	0	-0.8873125	0.554	0.801	0
Rpl13a	0	-0.8099290	0.766	0.917	0
Psat1	0	-1.6504466	0.090	0.308	0
Rps2	0	-1.0354959	0.541	0.786	0
P2ry13	0	1.1115332	0.837	0.701	0
Uba52rt	0	-1.0465813	0.507	0.755	0
Srgap2	0	1.1662103	0.837	0.638	0
Rplp0	0	-0.9526933	0.703	0.852	0
Or5v1	0	-4.0127099	0.035	0.197	0
Igf1	0	-3.0129862	0.149	0.367	0
Rpl23a	0	-1.1078486	0.396	0.686	0
Dpp7	0	-1.4386560	0.124	0.358	0
Aplp2	0	-1.4008564	0.181	0.434	0
Pkm	0	-1.3137763	0.382	0.642	0
Nceh1	0	-1.8755664	0.113	0.328	0
Rps23-ps1	0	-0.8477680	0.649	0.841	0
Fam20c	0	-2.6731972	0.055	0.227	0
Rps15	0	-1.1834704	0.498	0.725	0
Cd83	0	-1.5924008	0.363	0.629	0
Pld3	0	-1.2727364	0.294	0.557	0
Crip1	0	-2.5825650	0.084	0.273	0
Ftl1-ps1	0	-0.6357664	0.615	0.779	0
Rps29	0	-0.7011352	0.886	0.961	0

Microglia0_vs_Microglia2_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-11.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Cst7	0	-3.9686104	0.141	0.705	0
Apoe	0	-2.6506012	0.616	0.937	0
Clec7a	0	-2.8912634	0.138	0.668	0
Ccl3	0	-4.3531509	0.093	0.533	0
Lyz2	0	-1.9620885	0.636	0.921	0
Ctsb	0	-1.2553728	0.965	0.993	0
P2ry12	0	1.3417683	0.976	0.915	0
Axl	0	-2.6048608	0.106	0.533	0
Fth1	0	-1.1728108	0.952	0.983	0
Ctsz	0	-1.1364535	0.951	0.987	0
Ftl1	0	-1.0845956	0.948	0.976	0
B2m	0	-0.8841796	0.984	0.989	0
Ccl4	0	-5.4590391	0.041	0.332	0
Tmem119	0	1.3086498	0.951	0.760	0
Cd63	0	-1.5218787	0.675	0.893	0
Ctsd	0	-1.0327399	0.996	1.000	0
Lilrb4a	0	-4.0914589	0.050	0.345	0
Selplg	0	0.9323382	0.982	0.924	0
Baiap2l2	0	-3.2808146	0.015	0.238	0
Serinc3	0	0.7581640	0.984	0.976	0
Eef1a1	0	-0.9604677	0.946	0.989	0
Cox6a2	0	-3.6852880	0.034	0.282	0
Cd9	0	-1.0278271	0.918	0.969	0
Mif	0	-1.8511946	0.237	0.605	0
Tyrobp	0	-1.2701819	0.950	0.980	0
Npc2	0	-1.1582156	0.805	0.926	0
Rpl41	0	-1.2166273	0.773	0.930	0
Ank	0	-2.5357887	0.150	0.467	0
Cx3cr1	0	0.8703880	0.992	0.972	0
Lgals3bp	0	-1.5832710	0.433	0.758	0
Capg	0	-2.4097202	0.103	0.406	0
Itgax	0	-3.3825661	0.045	0.286	0
Malat1	0	0.5418416	0.992	0.952	0
Cd74	0	-2.4327293	0.130	0.443	0
Rpl18a	0	-0.9815482	0.873	0.952	0
Csf1	0	-2.9261667	0.052	0.301	0
Myo1e	0	-2.4967895	0.082	0.358	0
Cd52	0	-1.5075890	0.426	0.738	0
Cd68	0	-1.0343826	0.820	0.932	0
Rpl35rt	0	-1.1885764	0.731	0.915	0
Ccl6	0	-2.4365684	0.277	0.587	0
Ch25h	0	-4.4413136	0.015	0.201	0
Ctsl	0	-1.0159982	0.924	0.969	0
Ivns1abp	0	1.2930563	0.888	0.731	0
Gnas	0	-1.6204026	0.442	0.734	0
Ctss	0	-0.4719540	0.995	1.000	0
Hif1a	0	-1.5643552	0.262	0.587	0
Rplp1	0	-0.9466536	0.802	0.932	0
Gapdh	0	-1.2885205	0.661	0.841	0
Spp1	0	-7.7962458	0.017	0.177	0
Rpl21	0	-1.1188142	0.636	0.856	0
Rps28	0	-1.0568365	0.701	0.891	0
H2-D1	0	-0.8545038	0.831	0.941	0
Aldoa	0	-1.2316458	0.545	0.784	0
Rpl35	0	-1.0361363	0.760	0.928	0
Rpl32	0	-0.9739009	0.670	0.882	0
Rps18	0	-1.0264550	0.681	0.865	0
Ramp1	0	-2.0014110	0.123	0.380	0
Serpine2	0	-1.0954029	0.844	0.928	0
Uba52	0	-1.0300158	0.559	0.812	0
Anxa5	0	-1.9086755	0.131	0.389	0
Cpd	0	-1.7734823	0.094	0.328	0
Crlf2	0	-1.6833915	0.099	0.338	0
Nicol1	0	-2.8912067	0.022	0.179	0
Tpi1	0	-1.5549716	0.174	0.441	0
Rps16-ps2	0	-1.2757444	0.430	0.701	0
Mt1	0	-1.1482896	0.276	0.594	0
Wfdc17	0	-3.4174334	0.010	0.140	0
Ifi27l2a	0	-1.4590027	0.137	0.393	0
Lpl	0	-3.0948877	0.739	0.825	0
Rpl37a	0	-0.9054676	0.697	0.865	0
Maf	0	1.1640231	0.856	0.688	0
Zfp691	0	1.3945194	0.872	0.758	0
Tpt1	0	-1.1415396	0.618	0.825	0
Rps19	0	-0.9052618	0.703	0.871	0
Plaur	0	-2.6550672	0.085	0.290	0
Csf1r	0	0.4878526	0.991	0.991	0
Rpl10a	0	-0.8873125	0.554	0.801	0
Rpl13a	0	-0.8099290	0.766	0.917	0
Psat1	0	-1.6504466	0.090	0.308	0
Rps2	0	-1.0354959	0.541	0.786	0
P2ry13	0	1.1115332	0.837	0.701	0
Uba52rt	0	-1.0465813	0.507	0.755	0
Srgap2	0	1.1662103	0.837	0.638	0
Rplp0	0	-0.9526933	0.703	0.852	0
Or5v1	0	-4.0127099	0.035	0.197	0
Igf1	0	-3.0129862	0.149	0.367	0
Rpl23a	0	-1.1078486	0.396	0.686	0
Dpp7	0	-1.4386560	0.124	0.358	0
Aplp2	0	-1.4008564	0.181	0.434	0
Pkm	0	-1.3137763	0.382	0.642	0
Nceh1	0	-1.8755664	0.113	0.328	0
Rps23-ps1	0	-0.8477680	0.649	0.841	0
Fam20c	0	-2.6731972	0.055	0.227	0
Rps15	0	-1.1834704	0.498	0.725	0
Cd83	0	-1.5924008	0.363	0.629	0
Pld3	0	-1.2727364	0.294	0.557	0
Crip1	0	-2.5825650	0.084	0.273	0
Ftl1-ps1	0	-0.6357664	0.615	0.779	0
Rps29	0	-0.7011352	0.886	0.961	0

Microglia0_vs_Microglia3

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-14.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Rab3gap1	0	2.3200799	0.817	0.207	0
Ctsd	0	1.2598236	0.996	0.793	0
Slc38a6	0	1.2312242	0.893	0.369	0
Laptm5	0	1.2501469	0.982	0.665	0
Ppp2r5a	0	1.8225729	0.760	0.182	0
Inpp5d	0	0.7842893	0.879	0.355	0
Lair1	0	1.2800298	0.892	0.429	0
C1qa	0	1.0980093	0.993	0.675	0
C1qc	0	1.1052075	0.991	0.729	0
Olfml3	0	1.2549123	0.946	0.586	0
Noct	0	0.7950282	0.912	0.409	0
Grn	0	0.9498269	0.918	0.473	0
Csf1r	0	1.0462852	0.991	0.759	0
H2-D1	0	1.5873462	0.831	0.355	0
Pikfyve	0	0.6056509	0.847	0.296	0
Man2b1	0	0.8639139	0.875	0.399	0
Eif2a	0	-3.7447815	0.865	0.941	0
Serpine2	0	1.4775072	0.844	0.369	0
Trac	0	-4.8542294	0.660	0.823	0
Lipe	0	-3.8671953	0.851	0.975	0
Pag1	0	2.2174891	0.702	0.192	0
Scamp2	0	0.9552592	0.764	0.296	0
Ctsh	0	0.0368091	0.850	0.379	0
Krit1	0	1.1593111	0.891	0.404	0
Or13a17	0	-0.2890799	0.797	0.266	0
Cyth4	0	1.2490852	0.857	0.389	0
Ctsz	0	0.9088155	0.951	0.552	0
Ctsb	0	0.8587905	0.965	0.586	0
Selenop	0	0.7220140	0.941	0.512	0
Ctsa	0	0.6901389	0.925	0.502	0
Or6c208	0	2.3131314	0.675	0.158	0
Psap	0	0.8289519	0.972	0.626	0
Trem2	0	0.8711685	0.946	0.527	0
Nrros	0	0.4219785	0.762	0.261	0
Cyb5r4	0	2.3305416	0.733	0.212	0
Tmem119	0	1.0343938	0.951	0.576	0
Ubc	0	1.6796496	0.784	0.330	0
Vmn1r13	0	-4.5197170	0.834	0.946	0
Sfi1	0	1.7410775	0.762	0.291	0
Nom1	0	1.7834190	0.793	0.276	0
Cd9	0	1.0201080	0.918	0.537	0
Cpa6	0	1.0156069	0.760	0.217	0
Unc93b1	0	0.7158821	0.861	0.365	0
Ncf2	0	0.3044496	0.720	0.222	0
Tmbim6	0	1.3931614	0.821	0.365	0
Or10h28	0	0.6733835	0.790	0.256	0
Frmd4a	0	0.7927926	0.791	0.286	0
Chd9	0	0.1745577	0.928	0.433	0
Arhgef40	0	0.7038944	0.767	0.251	0
Nav2	0	2.2942769	0.770	0.296	0
Or52k2	0	1.6546740	0.703	0.202	0
Fyco1	0	1.4918146	0.682	0.182	0
Ifngr1	0	0.3134351	0.902	0.473	0
Pld4	0	1.1002495	0.908	0.498	0
Mef2c	0	1.1774500	0.787	0.310	0
Pkib	0	1.7546664	0.786	0.296	0
Dnajb14	0	2.0286524	0.668	0.177	0
Pdia3	0	0.9873904	0.785	0.325	0
Sirt5	0	1.1619146	0.804	0.330	0
Cx3cr1	0	0.8751947	0.992	0.704	0
Or1ab2	0	1.0569570	0.773	0.256	0
Tmem234	0	2.5641863	0.696	0.212	0
Rsrp1	0	0.6974994	0.924	0.468	0
Fcgr3	0	0.4645940	0.968	0.567	0
Nisch	0	1.5046671	0.797	0.335	0
Pan3	0	0.9867249	0.804	0.315	0
Vmn1r76	0	1.4066831	0.810	0.300	0
Vsir	0	0.8326679	0.938	0.532	0
Or13a18	0	0.5147844	0.844	0.350	0
Stab1	0	1.4345018	0.820	0.399	0
Csf3r	0	1.5151226	0.794	0.330	0
Bin1	0	0.5369929	0.729	0.227	0
Selplg	0	0.7874496	0.982	0.670	0
Fth1	0	0.4950527	0.952	0.581	0
Ubb	0	0.5284641	0.936	0.394	0
Ankrd17	0	1.4264851	0.730	0.261	0
Arhgap45	0	0.9233148	0.785	0.315	0
Acer3	0	1.6332087	0.772	0.296	0
Grk4	0	0.3649651	0.807	0.286	0
Hsp90b1	0	0.3003394	0.806	0.330	0
Arfgef3	0	-3.5194664	0.665	0.833	0
Elmo1	0	1.6432982	0.733	0.286	0
Ftl1	0	0.6317278	0.948	0.517	0
St14	0	0.5687877	0.671	0.177	0
Sirpa	0	0.9579991	0.945	0.542	0
Serinc3	0	0.6797207	0.984	0.714	0
Atp6v0b	0	1.2339277	0.760	0.291	0
Fus	0	1.3333049	0.778	0.335	0
Vmn1r197	0	0.0319971	0.785	0.296	0
Zfp738	0	0.5534946	0.831	0.345	0
Or1f19	0	0.8493404	0.800	0.305	0
Acad9	0	0.9169148	0.787	0.281	0
Pign	0	-0.1385837	0.810	0.315	0
Ly86	0	0.4635936	0.942	0.512	0
Lpcat2	0	0.4304866	0.909	0.463	0
Ppcdc	0	0.5652759	0.796	0.369	0
Tgfbr1	0	0.3172245	0.960	0.571	0
Tyrobp	0	0.9098924	0.950	0.562	0
Cux2	0	-3.7026818	0.808	0.906	0
Rbm25	0	0.3370216	0.850	0.394	0

Microglia0_vs_Microglia3_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-17.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Rab3gap1	0	2.3200799	0.817	0.207	0
Ctsd	0	1.2598236	0.996	0.793	0
Slc38a6	0	1.2312242	0.893	0.369	0
Laptm5	0	1.2501469	0.982	0.665	0
Ppp2r5a	0	1.8225729	0.760	0.182	0
Inpp5d	0	0.7842893	0.879	0.355	0
Lair1	0	1.2800298	0.892	0.429	0
C1qa	0	1.0980093	0.993	0.675	0
C1qc	0	1.1052075	0.991	0.729	0
Olfml3	0	1.2549123	0.946	0.586	0
Noct	0	0.7950282	0.912	0.409	0
Grn	0	0.9498269	0.918	0.473	0
Csf1r	0	1.0462852	0.991	0.759	0
H2-D1	0	1.5873462	0.831	0.355	0
Pikfyve	0	0.6056509	0.847	0.296	0
Man2b1	0	0.8639139	0.875	0.399	0
Eif2a	0	-3.7447815	0.865	0.941	0
Serpine2	0	1.4775072	0.844	0.369	0
Trac	0	-4.8542294	0.660	0.823	0
Lipe	0	-3.8671953	0.851	0.975	0
Pag1	0	2.2174891	0.702	0.192	0
Scamp2	0	0.9552592	0.764	0.296	0
Ctsh	0	0.0368091	0.850	0.379	0
Krit1	0	1.1593111	0.891	0.404	0
Or13a17	0	-0.2890799	0.797	0.266	0
Cyth4	0	1.2490852	0.857	0.389	0
Ctsz	0	0.9088155	0.951	0.552	0
Ctsb	0	0.8587905	0.965	0.586	0
Selenop	0	0.7220140	0.941	0.512	0
Ctsa	0	0.6901389	0.925	0.502	0
Or6c208	0	2.3131314	0.675	0.158	0
Psap	0	0.8289519	0.972	0.626	0
Trem2	0	0.8711685	0.946	0.527	0
Nrros	0	0.4219785	0.762	0.261	0
Cyb5r4	0	2.3305416	0.733	0.212	0
Tmem119	0	1.0343938	0.951	0.576	0
Ubc	0	1.6796496	0.784	0.330	0
Vmn1r13	0	-4.5197170	0.834	0.946	0
Sfi1	0	1.7410775	0.762	0.291	0
Nom1	0	1.7834190	0.793	0.276	0
Cd9	0	1.0201080	0.918	0.537	0
Cpa6	0	1.0156069	0.760	0.217	0
Unc93b1	0	0.7158821	0.861	0.365	0
Ncf2	0	0.3044496	0.720	0.222	0
Tmbim6	0	1.3931614	0.821	0.365	0
Or10h28	0	0.6733835	0.790	0.256	0
Frmd4a	0	0.7927926	0.791	0.286	0
Chd9	0	0.1745577	0.928	0.433	0
Arhgef40	0	0.7038944	0.767	0.251	0
Nav2	0	2.2942769	0.770	0.296	0
Or52k2	0	1.6546740	0.703	0.202	0
Fyco1	0	1.4918146	0.682	0.182	0
Ifngr1	0	0.3134351	0.902	0.473	0
Pld4	0	1.1002495	0.908	0.498	0
Mef2c	0	1.1774500	0.787	0.310	0
Pkib	0	1.7546664	0.786	0.296	0
Dnajb14	0	2.0286524	0.668	0.177	0
Pdia3	0	0.9873904	0.785	0.325	0
Sirt5	0	1.1619146	0.804	0.330	0
Cx3cr1	0	0.8751947	0.992	0.704	0
Or1ab2	0	1.0569570	0.773	0.256	0
Tmem234	0	2.5641863	0.696	0.212	0
Rsrp1	0	0.6974994	0.924	0.468	0
Fcgr3	0	0.4645940	0.968	0.567	0
Nisch	0	1.5046671	0.797	0.335	0
Pan3	0	0.9867249	0.804	0.315	0
Vmn1r76	0	1.4066831	0.810	0.300	0
Vsir	0	0.8326679	0.938	0.532	0
Or13a18	0	0.5147844	0.844	0.350	0
Stab1	0	1.4345018	0.820	0.399	0
Csf3r	0	1.5151226	0.794	0.330	0
Bin1	0	0.5369929	0.729	0.227	0
Selplg	0	0.7874496	0.982	0.670	0
Fth1	0	0.4950527	0.952	0.581	0
Ubb	0	0.5284641	0.936	0.394	0
Ankrd17	0	1.4264851	0.730	0.261	0
Arhgap45	0	0.9233148	0.785	0.315	0
Acer3	0	1.6332087	0.772	0.296	0
Grk4	0	0.3649651	0.807	0.286	0
Hsp90b1	0	0.3003394	0.806	0.330	0
Arfgef3	0	-3.5194664	0.665	0.833	0
Elmo1	0	1.6432982	0.733	0.286	0
Ftl1	0	0.6317278	0.948	0.517	0
St14	0	0.5687877	0.671	0.177	0
Sirpa	0	0.9579991	0.945	0.542	0
Serinc3	0	0.6797207	0.984	0.714	0
Atp6v0b	0	1.2339277	0.760	0.291	0
Fus	0	1.3333049	0.778	0.335	0
Vmn1r197	0	0.0319971	0.785	0.296	0
Zfp738	0	0.5534946	0.831	0.345	0
Or1f19	0	0.8493404	0.800	0.305	0
Acad9	0	0.9169148	0.787	0.281	0
Pign	0	-0.1385837	0.810	0.315	0
Ly86	0	0.4635936	0.942	0.512	0
Lpcat2	0	0.4304866	0.909	0.463	0
Ppcdc	0	0.5652759	0.796	0.369	0
Tgfbr1	0	0.3172245	0.960	0.571	0
Tyrobp	0	0.9098924	0.950	0.562	0
Cux2	0	-3.7026818	0.808	0.906	0
Rbm25	0	0.3370216	0.850	0.394	0

Microglia0_vs_Microglia4

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Ifit3	0e+00	-6.7519510	0.043	0.628	0.0000000
Ifit2	0e+00	-6.2509895	0.022	0.425	0.0000000
Ifi206	0e+00	-6.6172676	0.012	0.319	0.0000000
Rtp4	0e+00	-3.2501944	0.123	0.717	0.0000000
Oas2	0e+00	-4.6557561	0.018	0.327	0.0000000
Ifi207	0e+00	-4.2776523	0.025	0.354	0.0000000
Tgtp2	0e+00	-5.0102542	0.036	0.389	0.0000000
Ccl12	0e+00	-4.8412153	0.163	0.690	0.0000000
Ifitm3	0e+00	-3.6660454	0.099	0.566	0.0000000
Irf7	0e+00	-4.2309015	0.040	0.398	0.0000000
Oas1a	0e+00	-3.6459814	0.056	0.460	0.0000000
Usp18	0e+00	-4.1857036	0.079	0.504	0.0000000
Ifi211	0e+00	-6.6039944	0.018	0.283	0.0000000
Oasl2	0e+00	-5.1832898	0.204	0.673	0.0000000
Ifit3b	0e+00	-6.7944699	0.100	0.504	0.0000000
Oas1g	0e+00	-3.1817911	0.055	0.407	0.0000000
Stat1	0e+00	-2.9243892	0.333	0.823	0.0000000
Iigp1	0e+00	-5.8173255	0.134	0.558	0.0000000
Nlrc5	0e+00	-3.4188688	0.067	0.425	0.0000000
Mx1	0e+00	-4.9429243	0.131	0.522	0.0000000
Zbp1	0e+00	-4.9780860	0.056	0.363	0.0000000
Ifi209	0e+00	-4.0632897	0.106	0.469	0.0000000
Ifi27l2a	0e+00	-2.6566757	0.137	0.540	0.0000000
Phf11a	0e+00	-4.3457070	0.053	0.345	0.0000000
Iigp1c	0e+00	-3.6423472	0.203	0.602	0.0000000
Fgl2	0e+00	-2.9639154	0.092	0.442	0.0000000
Helz2	0e+00	-3.9479252	0.015	0.195	0.0000000
Ifit1	0e+00	-7.8531147	0.072	0.363	0.0000000
Samd9l	0e+00	-3.9798418	0.032	0.257	0.0000000
Cmpk2	0e+00	-4.6826237	0.009	0.159	0.0000000
Mx2	0e+00	-3.4230106	0.048	0.310	0.0000000
Lgals3bp	0e+00	-2.0021198	0.433	0.814	0.0000000
Phf11b	0e+00	-2.9683906	0.084	0.389	0.0000000
Ifi204	0e+00	-3.1791376	0.389	0.726	0.0000000
Rnf213	0e+00	-2.5455150	0.236	0.628	0.0000000
Trex1	0e+00	-2.0023779	0.203	0.575	0.0000000
Rsad2	0e+00	-5.7591202	0.070	0.319	0.0000000
Trim30a	0e+00	-1.7869126	0.362	0.726	0.0000000
Ifi205	0e+00	-2.7641257	0.016	0.159	0.0000000
Isg15	0e+00	-4.1544408	0.173	0.460	0.0000000
Trim30d	0e+00	-2.0439900	0.238	0.584	0.0000000
Ifi213	0e+00	-3.9631963	0.219	0.513	0.0000000
Slfn2	0e+00	-2.7613254	0.186	0.487	0.0000000
Ifi47	0e+00	-5.9605329	0.005	0.097	0.0000000
Ccl2	0e+00	-4.3963968	0.015	0.142	0.0000000
Oasl1	0e+00	-6.0440790	0.026	0.177	0.0000000
Phf11d	0e+00	-2.6600679	0.158	0.442	0.0000000
Ly6a	0e+00	-3.4065126	0.035	0.204	0.0000000
Parp12	0e+00	-1.8393088	0.137	0.416	0.0000000
B2m	0e+00	-0.6968649	0.984	1.000	0.0000000
Ifi208	0e+00	-3.5788855	0.183	0.469	0.0000000
Bst2	0e+00	-1.8245625	0.263	0.558	0.0000000
Isg20	0e+00	-2.6790339	0.035	0.195	0.0000000
Parp14	0e+00	-2.5719671	0.257	0.531	0.0000000
Herc6	0e+00	-2.8622272	0.429	0.681	0.0000000
Xaf1	0e+00	-2.5040517	0.481	0.708	0.0000000
Gbp9	0e+00	-2.2293329	0.075	0.283	0.0000000
Ddx60	0e+00	-2.3006137	0.133	0.381	0.0000000
Fcgr1	0e+00	-1.1529893	0.634	0.850	0.0000000
Tor3a	0e+00	-1.9524058	0.230	0.496	0.0000000
Sp100	0e+00	-2.7831339	0.375	0.611	0.0000000
Tgtp1	0e+00	-3.5557912	0.022	0.142	0.0000000
Axl	0e+00	-2.0141459	0.106	0.327	0.0000000
Etnk1	0e+00	-1.3333396	0.288	0.575	0.0000001
Gvin1	0e+00	-1.9487476	0.297	0.593	0.0000004
Slfn8	0e+00	-1.9722130	0.439	0.673	0.0000006
Irgm1	0e+00	-2.4908527	0.340	0.549	0.0000007
Ifih1	0e+00	-2.2804736	0.163	0.381	0.0000012
Ifi214	0e+00	-2.5325909	0.216	0.451	0.0000025
Ly6e	0e+00	-0.9653821	0.831	0.912	0.0000027
Dhx58	0e+00	-2.4560680	0.180	0.398	0.0000030
Znfx1	0e+00	-1.4570059	0.256	0.522	0.0000036
Ctss	0e+00	-0.3802187	0.995	1.000	0.0000046
Trim30c	0e+00	-4.9083411	0.013	0.097	0.0000080
Slfn5	0e+00	-3.0208370	0.527	0.717	0.0000101
Parp9	0e+00	-1.7350533	0.168	0.389	0.0000124
Nampt	0e+00	-1.4538988	0.095	0.283	0.0000136
Gvin3	0e+00	-1.3339944	0.062	0.221	0.0000156
Pml	0e+00	-1.9517895	0.133	0.336	0.0000183
Gvin-ps7	0e+00	-1.7278799	0.310	0.558	0.0000205
Psmb8	0e+00	-1.2938055	0.451	0.690	0.0000215
H2-D1	0e+00	-0.8769748	0.831	0.903	0.0000402
Stk-ps2	0e+00	-3.5651474	0.009	0.080	0.0000439
Ifi35	0e+00	-1.5238354	0.195	0.416	0.0000593
Il18bp	0e+00	-4.9709430	0.015	0.097	0.0000633
Gvin2	0e+00	-1.8304393	0.338	0.593	0.0000734
Uba7	0e+00	-1.3748398	0.247	0.487	0.0001701
Dtx3l	0e+00	-1.5000648	0.478	0.690	0.0002960
Gbp2	0e+00	-3.0519719	0.029	0.133	0.0003474
Nmi	0e+00	-1.4919321	0.113	0.292	0.0004628
H2-K1	0e+00	-0.9577947	0.778	0.841	0.0004653
Socs1	0e+00	-2.0940465	0.022	0.115	0.0005418
Epsti1	0e+00	-1.7535665	0.141	0.336	0.0005803
Sdc3	0e+00	-1.5345282	0.116	0.292	0.0006269
Csf1	1e-07	-2.5333990	0.052	0.177	0.0009569
Igtp	1e-07	-1.8254598	0.236	0.434	0.0010707
Tcstv4	1e-07	-2.7218314	0.028	0.124	0.0014691
Ogfr	1e-07	-1.1826233	0.104	0.274	0.0015311
Scimp	1e-07	-2.6625806	0.035	0.142	0.0017639
P2ry12	3e-07	0.5307100	0.976	0.965	0.0044757

Microglia0_vs_Microglia4_comorbid

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Ifit3	0e+00	-6.7519510	0.043	0.628	0.0000000
Ifit2	0e+00	-6.2509895	0.022	0.425	0.0000000
Ifi206	0e+00	-6.6172676	0.012	0.319	0.0000000
Rtp4	0e+00	-3.2501944	0.123	0.717	0.0000000
Oas2	0e+00	-4.6557561	0.018	0.327	0.0000000
Ifi207	0e+00	-4.2776523	0.025	0.354	0.0000000
Tgtp2	0e+00	-5.0102542	0.036	0.389	0.0000000
Ccl12	0e+00	-4.8412153	0.163	0.690	0.0000000
Ifitm3	0e+00	-3.6660454	0.099	0.566	0.0000000
Irf7	0e+00	-4.2309015	0.040	0.398	0.0000000
Oas1a	0e+00	-3.6459814	0.056	0.460	0.0000000
Usp18	0e+00	-4.1857036	0.079	0.504	0.0000000
Ifi211	0e+00	-6.6039944	0.018	0.283	0.0000000
Oasl2	0e+00	-5.1832898	0.204	0.673	0.0000000
Ifit3b	0e+00	-6.7944699	0.100	0.504	0.0000000
Oas1g	0e+00	-3.1817911	0.055	0.407	0.0000000
Stat1	0e+00	-2.9243892	0.333	0.823	0.0000000
Iigp1	0e+00	-5.8173255	0.134	0.558	0.0000000
Nlrc5	0e+00	-3.4188688	0.067	0.425	0.0000000
Mx1	0e+00	-4.9429243	0.131	0.522	0.0000000
Zbp1	0e+00	-4.9780860	0.056	0.363	0.0000000
Ifi209	0e+00	-4.0632897	0.106	0.469	0.0000000
Ifi27l2a	0e+00	-2.6566757	0.137	0.540	0.0000000
Phf11a	0e+00	-4.3457070	0.053	0.345	0.0000000
Iigp1c	0e+00	-3.6423472	0.203	0.602	0.0000000
Fgl2	0e+00	-2.9639154	0.092	0.442	0.0000000
Helz2	0e+00	-3.9479252	0.015	0.195	0.0000000
Ifit1	0e+00	-7.8531147	0.072	0.363	0.0000000
Samd9l	0e+00	-3.9798418	0.032	0.257	0.0000000
Cmpk2	0e+00	-4.6826237	0.009	0.159	0.0000000
Mx2	0e+00	-3.4230106	0.048	0.310	0.0000000
Lgals3bp	0e+00	-2.0021198	0.433	0.814	0.0000000
Phf11b	0e+00	-2.9683906	0.084	0.389	0.0000000
Ifi204	0e+00	-3.1791376	0.389	0.726	0.0000000
Rnf213	0e+00	-2.5455150	0.236	0.628	0.0000000
Trex1	0e+00	-2.0023779	0.203	0.575	0.0000000
Rsad2	0e+00	-5.7591202	0.070	0.319	0.0000000
Trim30a	0e+00	-1.7869126	0.362	0.726	0.0000000
Ifi205	0e+00	-2.7641257	0.016	0.159	0.0000000
Isg15	0e+00	-4.1544408	0.173	0.460	0.0000000
Trim30d	0e+00	-2.0439900	0.238	0.584	0.0000000
Ifi213	0e+00	-3.9631963	0.219	0.513	0.0000000
Slfn2	0e+00	-2.7613254	0.186	0.487	0.0000000
Ifi47	0e+00	-5.9605329	0.005	0.097	0.0000000
Ccl2	0e+00	-4.3963968	0.015	0.142	0.0000000
Oasl1	0e+00	-6.0440790	0.026	0.177	0.0000000
Phf11d	0e+00	-2.6600679	0.158	0.442	0.0000000
Ly6a	0e+00	-3.4065126	0.035	0.204	0.0000000
Parp12	0e+00	-1.8393088	0.137	0.416	0.0000000
B2m	0e+00	-0.6968649	0.984	1.000	0.0000000
Ifi208	0e+00	-3.5788855	0.183	0.469	0.0000000
Bst2	0e+00	-1.8245625	0.263	0.558	0.0000000
Isg20	0e+00	-2.6790339	0.035	0.195	0.0000000
Parp14	0e+00	-2.5719671	0.257	0.531	0.0000000
Herc6	0e+00	-2.8622272	0.429	0.681	0.0000000
Xaf1	0e+00	-2.5040517	0.481	0.708	0.0000000
Gbp9	0e+00	-2.2293329	0.075	0.283	0.0000000
Ddx60	0e+00	-2.3006137	0.133	0.381	0.0000000
Fcgr1	0e+00	-1.1529893	0.634	0.850	0.0000000
Tor3a	0e+00	-1.9524058	0.230	0.496	0.0000000
Sp100	0e+00	-2.7831339	0.375	0.611	0.0000000
Tgtp1	0e+00	-3.5557912	0.022	0.142	0.0000000
Axl	0e+00	-2.0141459	0.106	0.327	0.0000000
Etnk1	0e+00	-1.3333396	0.288	0.575	0.0000001
Gvin1	0e+00	-1.9487476	0.297	0.593	0.0000004
Slfn8	0e+00	-1.9722130	0.439	0.673	0.0000006
Irgm1	0e+00	-2.4908527	0.340	0.549	0.0000007
Ifih1	0e+00	-2.2804736	0.163	0.381	0.0000012
Ifi214	0e+00	-2.5325909	0.216	0.451	0.0000025
Ly6e	0e+00	-0.9653821	0.831	0.912	0.0000027
Dhx58	0e+00	-2.4560680	0.180	0.398	0.0000030
Znfx1	0e+00	-1.4570059	0.256	0.522	0.0000036
Ctss	0e+00	-0.3802187	0.995	1.000	0.0000046
Trim30c	0e+00	-4.9083411	0.013	0.097	0.0000080
Slfn5	0e+00	-3.0208370	0.527	0.717	0.0000101
Parp9	0e+00	-1.7350533	0.168	0.389	0.0000124
Nampt	0e+00	-1.4538988	0.095	0.283	0.0000136
Gvin3	0e+00	-1.3339944	0.062	0.221	0.0000156
Pml	0e+00	-1.9517895	0.133	0.336	0.0000183
Gvin-ps7	0e+00	-1.7278799	0.310	0.558	0.0000205
Psmb8	0e+00	-1.2938055	0.451	0.690	0.0000215
H2-D1	0e+00	-0.8769748	0.831	0.903	0.0000402
Stk-ps2	0e+00	-3.5651474	0.009	0.080	0.0000439
Ifi35	0e+00	-1.5238354	0.195	0.416	0.0000593
Il18bp	0e+00	-4.9709430	0.015	0.097	0.0000633
Gvin2	0e+00	-1.8304393	0.338	0.593	0.0000734
Uba7	0e+00	-1.3748398	0.247	0.487	0.0001701
Dtx3l	0e+00	-1.5000648	0.478	0.690	0.0002960
Gbp2	0e+00	-3.0519719	0.029	0.133	0.0003474
Nmi	0e+00	-1.4919321	0.113	0.292	0.0004628
H2-K1	0e+00	-0.9577947	0.778	0.841	0.0004653
Socs1	0e+00	-2.0940465	0.022	0.115	0.0005418
Epsti1	0e+00	-1.7535665	0.141	0.336	0.0005803
Sdc3	0e+00	-1.5345282	0.116	0.292	0.0006269
Csf1	1e-07	-2.5333990	0.052	0.177	0.0009569
Igtp	1e-07	-1.8254598	0.236	0.434	0.0010707
Tcstv4	1e-07	-2.7218314	0.028	0.124	0.0014691
Ogfr	1e-07	-1.1826233	0.104	0.274	0.0015311
Scimp	1e-07	-2.6625806	0.035	0.142	0.0017639
P2ry12	3e-07	0.5307100	0.976	0.965	0.0044757

Microglia0_vs_Microglia5

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0000000	-7.4318523	0.049	0.904	0.0000000
H2-Eb1	0.0000000	-8.6687759	0.017	0.630	0.0000000
Cd74	0.0000000	-7.2094994	0.130	0.959	0.0000000
H2-Aa	0.0000000	-8.4606111	0.103	0.712	0.0000000
H2-D1	0.0000000	-1.8190616	0.831	0.959	0.0000000
H2-K1	0.0000000	-1.4638914	0.778	0.932	0.0000000
Ctss	0.0000000	-0.5001659	0.995	1.000	0.0000101
H2-Oa	0.0000000	-1.9985115	0.115	0.356	0.0000127
Itgax	0.0000000	-3.1706542	0.045	0.205	0.0000154
Wfdc17	0.0000000	-2.8723306	0.010	0.096	0.0000430
B2m	0.0000000	-0.7917514	0.984	0.986	0.0003590
H2-T11-ps	0.0000000	-0.7227747	0.105	0.315	0.0004487
Pfkm	0.0000000	-3.0047665	0.008	0.082	0.0005098
Cox6a2	0.0000000	-2.7826451	0.034	0.164	0.0006196
Spp1	0.0000001	-7.5562557	0.017	0.110	0.0014588
Egln3	0.0000001	-2.3085412	0.006	0.068	0.0015874
Nbl1	0.0000001	-3.9810403	0.013	0.096	0.0022861
Stab1	0.0000002	1.4428220	0.820	0.616	0.0032953
Axl	0.0000005	-1.4711972	0.106	0.301	0.0074292
Fgl2	0.0000006	-1.6909638	0.092	0.274	0.0095163
Baiap2l2	0.0000013	-2.8536934	0.015	0.096	0.0209162
Hpse	0.0000015	-3.9991735	0.012	0.082	0.0240343
Usp12	0.0000018	-1.5575384	0.200	0.425	0.0293490
Tcap	0.0000022	-5.0279818	0.001	0.027	0.0351516
Ly86	0.0000022	-0.5983349	0.942	0.986	0.0352783
Capg	0.0000034	-2.0517585	0.103	0.274	0.0546797
Znrf3	0.0000037	0.9214717	0.881	0.753	0.0582910
Ccl6	0.0000037	-1.8924277	0.277	0.507	0.0591855
BC106179	0.0000040	1.4987526	0.341	0.082	0.0643132
Ccl3	0.0000041	-1.3728799	0.093	0.260	0.0652644
Mmp12	0.0000047	1.6091279	0.594	0.315	0.0754457
H2-T23	0.0000071	-1.1910011	0.658	0.808	0.1130697
Cst7	0.0000112	-2.9623410	0.141	0.301	0.1782549
Ecscr	0.0000118	1.6802238	0.440	0.178	0.1881133
H2-Q5	0.0000119	-1.9830854	0.143	0.315	0.1892146
Tspo	0.0000120	-0.8627031	0.182	0.397	0.1909594
Mtss1	0.0000128	1.4973518	0.691	0.507	0.2035896
Nfia	0.0000144	0.7716806	0.843	0.685	0.2300119
Nox4	0.0000154	1.9389200	0.600	0.356	0.2451486
H2-M3	0.0000155	-1.3374537	0.208	0.411	0.2470730
Atp1a3	0.0000158	-1.2609123	0.102	0.260	0.2517892
Zfp369	0.0000262	1.2163604	0.871	0.753	0.4179872
Prr15	0.0000264	2.1017396	0.758	0.616	0.4215049
Vmn1r76	0.0000265	1.1382475	0.810	0.562	0.4220682
H2-Q7	0.0000266	-2.5869970	0.468	0.603	0.4236276
Rb1	0.0000296	1.3468121	0.505	0.274	0.4719877
Psap	0.0000325	-0.4932126	0.972	0.986	0.5188936
Slc25a23	0.0000343	3.0365508	0.309	0.082	0.5475530
Ly6e	0.0000347	-0.8385618	0.831	0.863	0.5529564
Ramp1	0.0000355	-1.3487439	0.123	0.288	0.5660729
Samd9l	0.0000410	-2.3460644	0.032	0.123	0.6536817
Or51q1	0.0000415	1.2831293	0.922	0.795	0.6620993
H2-Q6	0.0000417	-1.6910464	0.295	0.493	0.6655392
Dcstamp	0.0000424	-2.5445271	0.007	0.055	0.6758766
Jcad	0.0000427	-2.4455102	0.007	0.055	0.6811751
Serpine2	0.0000539	-0.6868904	0.844	0.904	0.8593515
Itpripl1	0.0000606	1.1461761	0.538	0.301	0.9664142
Adora1	0.0000610	-1.8310104	0.021	0.096	0.9729686
Traf5	0.0000654	1.2367323	0.794	0.616	1.0000000
Sh2d6	0.0000742	-3.1697959	0.012	0.068	1.0000000
Krt7	0.0000754	1.2661316	0.502	0.274	1.0000000
Serinc3	0.0000852	0.3650067	0.984	0.986	1.0000000
Bltp1	0.0000983	0.7262640	0.713	0.466	1.0000000
H2-Q10	0.0001118	-0.3725134	0.421	0.630	1.0000000
Gcn1	0.0001227	1.5491535	0.775	0.630	1.0000000
Zfp738	0.0001349	0.9844280	0.831	0.685	1.0000000
Tsc22d1	0.0001463	-3.2987462	0.042	0.137	1.0000000
Clec7a	0.0001509	-1.7652091	0.138	0.288	1.0000000
Nav2	0.0001628	0.8146888	0.770	0.616	1.0000000
Tubb4a	0.0001692	-3.6385477	0.005	0.041	1.0000000
Mrgpre	0.0001697	0.1276763	0.467	0.233	1.0000000
Crym	0.0001767	-3.5251688	0.005	0.041	1.0000000
Spcs1	0.0001772	-0.9868105	0.369	0.589	1.0000000
Ctsb	0.0001814	-0.6662170	0.965	0.959	1.0000000
Syngr1	0.0001869	-0.8051675	0.676	0.753	1.0000000
C1qa	0.0001884	-0.2906556	0.993	1.000	1.0000000
Grk4	0.0001968	1.1218519	0.807	0.630	1.0000000
Acnat1	0.0002074	1.1854870	0.758	0.616	1.0000000
Dido1	0.0002100	0.7600088	0.846	0.712	1.0000000
Pdcd1	0.0002302	-1.7021805	0.036	0.123	1.0000000
Ank3	0.0002332	1.6094905	0.330	0.123	1.0000000
Or8b44	0.0002783	1.3357253	0.804	0.726	1.0000000
Lpar6	0.0002814	0.9389916	0.690	0.479	1.0000000
C1qb	0.0003041	-0.3651707	0.988	0.986	1.0000000
Eef1a1	0.0003166	-0.5130744	0.946	0.945	1.0000000
Nipal2	0.0003181	1.2702075	0.817	0.712	1.0000000
Bora	0.0003303	1.4568299	0.504	0.274	1.0000000
Klhl32	0.0003304	2.1733449	0.433	0.260	1.0000000
Or4m1	0.0003624	1.3325952	0.501	0.288	1.0000000
Or14j9	0.0003854	-4.3027381	0.009	0.055	1.0000000
Haus8	0.0003947	1.1059810	0.757	0.562	1.0000000
Npc2	0.0003960	-0.7483326	0.805	0.849	1.0000000
Fbxo47	0.0004025	-2.9745836	0.009	0.055	1.0000000
Vwa3b	0.0004033	-3.5834292	0.014	0.068	1.0000000
Csf1	0.0004128	-1.5268798	0.052	0.151	1.0000000
Lrrc8b	0.0004415	-1.6023763	0.009	0.055	1.0000000
Vmn1r26	0.0004489	0.9660346	0.743	0.548	1.0000000
Rps2-ps10	0.0004499	2.3088525	0.736	0.589	1.0000000
Parva	0.0004669	1.6365744	0.522	0.329	1.0000000
Il3ra	0.0004705	-1.4855578	0.019	0.082	1.0000000

Microglia0_vs_Microglia5_comorbid

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0000000	-7.4318523	0.049	0.904	0.0000000
H2-Eb1	0.0000000	-8.6687759	0.017	0.630	0.0000000
Cd74	0.0000000	-7.2094994	0.130	0.959	0.0000000
H2-Aa	0.0000000	-8.4606111	0.103	0.712	0.0000000
H2-D1	0.0000000	-1.8190616	0.831	0.959	0.0000000
H2-K1	0.0000000	-1.4638914	0.778	0.932	0.0000000
Ctss	0.0000000	-0.5001659	0.995	1.000	0.0000101
H2-Oa	0.0000000	-1.9985115	0.115	0.356	0.0000127
Itgax	0.0000000	-3.1706542	0.045	0.205	0.0000154
Wfdc17	0.0000000	-2.8723306	0.010	0.096	0.0000430
B2m	0.0000000	-0.7917514	0.984	0.986	0.0003590
H2-T11-ps	0.0000000	-0.7227747	0.105	0.315	0.0004487
Pfkm	0.0000000	-3.0047665	0.008	0.082	0.0005098
Cox6a2	0.0000000	-2.7826451	0.034	0.164	0.0006196
Spp1	0.0000001	-7.5562557	0.017	0.110	0.0014588
Egln3	0.0000001	-2.3085412	0.006	0.068	0.0015874
Nbl1	0.0000001	-3.9810403	0.013	0.096	0.0022861
Stab1	0.0000002	1.4428220	0.820	0.616	0.0032953
Axl	0.0000005	-1.4711972	0.106	0.301	0.0074292
Fgl2	0.0000006	-1.6909638	0.092	0.274	0.0095163
Baiap2l2	0.0000013	-2.8536934	0.015	0.096	0.0209162
Hpse	0.0000015	-3.9991735	0.012	0.082	0.0240343
Usp12	0.0000018	-1.5575384	0.200	0.425	0.0293490
Tcap	0.0000022	-5.0279818	0.001	0.027	0.0351516
Ly86	0.0000022	-0.5983349	0.942	0.986	0.0352783
Capg	0.0000034	-2.0517585	0.103	0.274	0.0546797
Znrf3	0.0000037	0.9214717	0.881	0.753	0.0582910
Ccl6	0.0000037	-1.8924277	0.277	0.507	0.0591855
BC106179	0.0000040	1.4987526	0.341	0.082	0.0643132
Ccl3	0.0000041	-1.3728799	0.093	0.260	0.0652644
Mmp12	0.0000047	1.6091279	0.594	0.315	0.0754457
H2-T23	0.0000071	-1.1910011	0.658	0.808	0.1130697
Cst7	0.0000112	-2.9623410	0.141	0.301	0.1782549
Ecscr	0.0000118	1.6802238	0.440	0.178	0.1881133
H2-Q5	0.0000119	-1.9830854	0.143	0.315	0.1892146
Tspo	0.0000120	-0.8627031	0.182	0.397	0.1909594
Mtss1	0.0000128	1.4973518	0.691	0.507	0.2035896
Nfia	0.0000144	0.7716806	0.843	0.685	0.2300119
Nox4	0.0000154	1.9389200	0.600	0.356	0.2451486
H2-M3	0.0000155	-1.3374537	0.208	0.411	0.2470730
Atp1a3	0.0000158	-1.2609123	0.102	0.260	0.2517892
Zfp369	0.0000262	1.2163604	0.871	0.753	0.4179872
Prr15	0.0000264	2.1017396	0.758	0.616	0.4215049
Vmn1r76	0.0000265	1.1382475	0.810	0.562	0.4220682
H2-Q7	0.0000266	-2.5869970	0.468	0.603	0.4236276
Rb1	0.0000296	1.3468121	0.505	0.274	0.4719877
Psap	0.0000325	-0.4932126	0.972	0.986	0.5188936
Slc25a23	0.0000343	3.0365508	0.309	0.082	0.5475530
Ly6e	0.0000347	-0.8385618	0.831	0.863	0.5529564
Ramp1	0.0000355	-1.3487439	0.123	0.288	0.5660729
Samd9l	0.0000410	-2.3460644	0.032	0.123	0.6536817
Or51q1	0.0000415	1.2831293	0.922	0.795	0.6620993
H2-Q6	0.0000417	-1.6910464	0.295	0.493	0.6655392
Dcstamp	0.0000424	-2.5445271	0.007	0.055	0.6758766
Jcad	0.0000427	-2.4455102	0.007	0.055	0.6811751
Serpine2	0.0000539	-0.6868904	0.844	0.904	0.8593515
Itpripl1	0.0000606	1.1461761	0.538	0.301	0.9664142
Adora1	0.0000610	-1.8310104	0.021	0.096	0.9729686
Traf5	0.0000654	1.2367323	0.794	0.616	1.0000000
Sh2d6	0.0000742	-3.1697959	0.012	0.068	1.0000000
Krt7	0.0000754	1.2661316	0.502	0.274	1.0000000
Serinc3	0.0000852	0.3650067	0.984	0.986	1.0000000
Bltp1	0.0000983	0.7262640	0.713	0.466	1.0000000
H2-Q10	0.0001118	-0.3725134	0.421	0.630	1.0000000
Gcn1	0.0001227	1.5491535	0.775	0.630	1.0000000
Zfp738	0.0001349	0.9844280	0.831	0.685	1.0000000
Tsc22d1	0.0001463	-3.2987462	0.042	0.137	1.0000000
Clec7a	0.0001509	-1.7652091	0.138	0.288	1.0000000
Nav2	0.0001628	0.8146888	0.770	0.616	1.0000000
Tubb4a	0.0001692	-3.6385477	0.005	0.041	1.0000000
Mrgpre	0.0001697	0.1276763	0.467	0.233	1.0000000
Crym	0.0001767	-3.5251688	0.005	0.041	1.0000000
Spcs1	0.0001772	-0.9868105	0.369	0.589	1.0000000
Ctsb	0.0001814	-0.6662170	0.965	0.959	1.0000000
Syngr1	0.0001869	-0.8051675	0.676	0.753	1.0000000
C1qa	0.0001884	-0.2906556	0.993	1.000	1.0000000
Grk4	0.0001968	1.1218519	0.807	0.630	1.0000000
Acnat1	0.0002074	1.1854870	0.758	0.616	1.0000000
Dido1	0.0002100	0.7600088	0.846	0.712	1.0000000
Pdcd1	0.0002302	-1.7021805	0.036	0.123	1.0000000
Ank3	0.0002332	1.6094905	0.330	0.123	1.0000000
Or8b44	0.0002783	1.3357253	0.804	0.726	1.0000000
Lpar6	0.0002814	0.9389916	0.690	0.479	1.0000000
C1qb	0.0003041	-0.3651707	0.988	0.986	1.0000000
Eef1a1	0.0003166	-0.5130744	0.946	0.945	1.0000000
Nipal2	0.0003181	1.2702075	0.817	0.712	1.0000000
Bora	0.0003303	1.4568299	0.504	0.274	1.0000000
Klhl32	0.0003304	2.1733449	0.433	0.260	1.0000000
Or4m1	0.0003624	1.3325952	0.501	0.288	1.0000000
Or14j9	0.0003854	-4.3027381	0.009	0.055	1.0000000
Haus8	0.0003947	1.1059810	0.757	0.562	1.0000000
Npc2	0.0003960	-0.7483326	0.805	0.849	1.0000000
Fbxo47	0.0004025	-2.9745836	0.009	0.055	1.0000000
Vwa3b	0.0004033	-3.5834292	0.014	0.068	1.0000000
Csf1	0.0004128	-1.5268798	0.052	0.151	1.0000000
Lrrc8b	0.0004415	-1.6023763	0.009	0.055	1.0000000
Vmn1r26	0.0004489	0.9660346	0.743	0.548	1.0000000
Rps2-ps10	0.0004499	2.3088525	0.736	0.589	1.0000000
Parva	0.0004669	1.6365744	0.522	0.329	1.0000000
Il3ra	0.0004705	-1.4855578	0.019	0.082	1.0000000

Microglia1_vs_Microglia2

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Cst7	0	-5.2302997	0.089	0.705	0
Clec7a	0	-3.7205517	0.081	0.668	0
Apoe	0	-2.6626949	0.578	0.937	0
Lyz2	0	-2.1110446	0.518	0.921	0
Ccl3	0	-4.3253455	0.048	0.533	0
Ctsb	0	-1.4917025	0.876	0.993	0
Ctsd	0	-1.3683941	0.954	1.000	0
Axl	0	-3.1095888	0.073	0.533	0
Ctsz	0	-1.3585033	0.837	0.987	0
Cd63	0	-1.6382595	0.511	0.893	0
Lgals3bp	0	-2.1562683	0.315	0.758	0
Ank	0	-3.9303173	0.066	0.467	0
Ftl1	0	-1.2109756	0.837	0.976	0
Tyrobp	0	-1.5660059	0.815	0.980	0
Fth1	0	-1.1654732	0.847	0.983	0
Mif	0	-1.7946341	0.149	0.605	0
P2ry12	0	1.4191441	0.949	0.915	0
B2m	0	-0.8797025	0.949	0.989	0
Malat1	0	0.8542927	0.987	0.952	0
Rps16-ps2	0	-1.7881802	0.255	0.701	0
Gnas	0	-1.5854706	0.305	0.734	0
Lpl	0	-3.4413178	0.541	0.825	0
Ccl4	0	-6.6339512	0.026	0.332	0
Rpl10a-ps1	0	-1.9408953	0.133	0.528	0
Hif1a	0	-1.7572560	0.170	0.587	0
Ccl6	0	-2.5067937	0.194	0.587	0
Aldoa	0	-1.5312118	0.359	0.784	0
Capg	0	-2.8656229	0.063	0.406	0
Trac	0	2.1917910	0.869	0.568	0
Cd52	0	-1.2581163	0.292	0.738	0
Gapdh	0	-1.4627889	0.487	0.841	0
Cd9	0	-1.1027383	0.800	0.969	0
Npc2	0	-1.0907539	0.676	0.926	0
Pkm	0	-1.5299422	0.242	0.642	0
Lilrb4a	0	-3.3405404	0.043	0.345	0
Cd74	0	-2.4981197	0.096	0.443	0
Arfgef3	0	1.5791000	0.874	0.574	0
Cd68	0	-1.0498472	0.690	0.932	0
Ifi27l2a	0	-2.0662952	0.074	0.393	0
Baiap2l2	0	-5.9736114	0.006	0.238	0
Eef1a1	0	-0.7849778	0.884	0.989	0
Ctsl	0	-1.0043141	0.796	0.969	0
Myo1e	0	-2.6605331	0.059	0.358	0
Anxa5	0	-2.4724416	0.079	0.389	0
Cox6a2	0	-2.6062141	0.024	0.282	0
H2-D1	0	-0.9365601	0.706	0.941	0
Syngr1	0	-1.4104739	0.482	0.810	0
Cux2	0	1.4455124	0.924	0.821	0
Rps12l1	0	-1.5296697	0.295	0.629	0
Rps13-ps2	0	-2.1192775	0.098	0.410	0
Rps2	0	-1.0391815	0.393	0.786	0
Mt1	0	-0.9889788	0.196	0.594	0
Lipe	0	1.5878442	0.935	0.830	0
Ramp1	0	-2.0524426	0.080	0.380	0
Itgax	0	-2.8686871	0.033	0.286	0
Pld3	0	-1.5493614	0.199	0.557	0
Csf1	0	-2.5105916	0.040	0.301	0
Rplp0	0	-0.9805014	0.543	0.852	0
Rps16	0	-0.9344615	0.444	0.817	0
Atp6v0c	0	-1.0388843	0.507	0.838	0
Psat1	0	-1.5343347	0.048	0.308	0
Tpi1	0	-1.4365039	0.116	0.441	0
Rps5	0	-1.0254345	0.315	0.679	0
Rpl18a	0	-0.7951908	0.767	0.952	0
Ucp2	0	-1.4129656	0.210	0.555	0
Pax6	0	1.6359616	0.846	0.611	0
Tpd52	0	-1.2310377	0.297	0.633	0
Cadm1	0	-1.1234179	0.297	0.651	0
Rpl41	0	-0.8072862	0.617	0.930	0
Ch25h	0	-5.2138413	0.008	0.201	0
Nceh1	0	-2.4527022	0.068	0.328	0
Cd83	0	-1.2975712	0.279	0.629	0
Igf1	0	-4.3451636	0.101	0.367	0
Rpl21	0	-0.7645073	0.506	0.856	0
Rps18	0	-0.7996990	0.554	0.865	0
Eef1b2	0	-0.7655968	0.262	0.618	0
Rpl19	0	-0.8146156	0.399	0.766	0
Rpsa	0	-1.0583222	0.293	0.629	0
Gusb	0	-1.0060868	0.522	0.793	0
Rbm45	0	1.6865553	0.841	0.594	0
Vmn1r13	0	1.0814302	0.914	0.758	0
Rpl26	0	-0.7333611	0.437	0.803	0
Uba52rt	0	-0.7772868	0.388	0.755	0
Rpl29	0	-0.7505988	0.227	0.561	0
Crlf2	0	-1.4283320	0.071	0.338	0
Rpl10-ps3	0	-1.2431144	0.409	0.718	0
Rps26-ps1	0	-1.6984930	0.135	0.419	0
Hexa	0	-0.9791101	0.662	0.904	0
Ndufa2	0	-0.6319746	0.195	0.541	0
Lamp1	0	-0.8093437	0.680	0.915	0
Aplp2	0	-1.2985348	0.134	0.434	0
Tmem119	0	1.2017092	0.872	0.760	0
Lilrb4b	0	-1.0860176	0.038	0.264	0
Fam20c	0	-3.0711934	0.026	0.227	0
Tpt1-ps3	0	-1.0787850	0.225	0.561	0
Rpl28-ps1	0	-0.3789046	0.159	0.483	0
Rps13	0	-0.5005972	0.295	0.655	0
Serpine2	0	-0.8796995	0.701	0.928	0
Galntl6	0	1.8506210	0.867	0.609	0
Rps25	0	-0.5945093	0.615	0.865	0

Microglia1_vs_Microglia2_comorbid

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Cst7	0	-5.2302997	0.089	0.705	0
Clec7a	0	-3.7205517	0.081	0.668	0
Apoe	0	-2.6626949	0.578	0.937	0
Lyz2	0	-2.1110446	0.518	0.921	0
Ccl3	0	-4.3253455	0.048	0.533	0
Ctsb	0	-1.4917025	0.876	0.993	0
Ctsd	0	-1.3683941	0.954	1.000	0
Axl	0	-3.1095888	0.073	0.533	0
Ctsz	0	-1.3585033	0.837	0.987	0
Cd63	0	-1.6382595	0.511	0.893	0
Lgals3bp	0	-2.1562683	0.315	0.758	0
Ank	0	-3.9303173	0.066	0.467	0
Ftl1	0	-1.2109756	0.837	0.976	0
Tyrobp	0	-1.5660059	0.815	0.980	0
Fth1	0	-1.1654732	0.847	0.983	0
Mif	0	-1.7946341	0.149	0.605	0
P2ry12	0	1.4191441	0.949	0.915	0
B2m	0	-0.8797025	0.949	0.989	0
Malat1	0	0.8542927	0.987	0.952	0
Rps16-ps2	0	-1.7881802	0.255	0.701	0
Gnas	0	-1.5854706	0.305	0.734	0
Lpl	0	-3.4413178	0.541	0.825	0
Ccl4	0	-6.6339512	0.026	0.332	0
Rpl10a-ps1	0	-1.9408953	0.133	0.528	0
Hif1a	0	-1.7572560	0.170	0.587	0
Ccl6	0	-2.5067937	0.194	0.587	0
Aldoa	0	-1.5312118	0.359	0.784	0
Capg	0	-2.8656229	0.063	0.406	0
Trac	0	2.1917910	0.869	0.568	0
Cd52	0	-1.2581163	0.292	0.738	0
Gapdh	0	-1.4627889	0.487	0.841	0
Cd9	0	-1.1027383	0.800	0.969	0
Npc2	0	-1.0907539	0.676	0.926	0
Pkm	0	-1.5299422	0.242	0.642	0
Lilrb4a	0	-3.3405404	0.043	0.345	0
Cd74	0	-2.4981197	0.096	0.443	0
Arfgef3	0	1.5791000	0.874	0.574	0
Cd68	0	-1.0498472	0.690	0.932	0
Ifi27l2a	0	-2.0662952	0.074	0.393	0
Baiap2l2	0	-5.9736114	0.006	0.238	0
Eef1a1	0	-0.7849778	0.884	0.989	0
Ctsl	0	-1.0043141	0.796	0.969	0
Myo1e	0	-2.6605331	0.059	0.358	0
Anxa5	0	-2.4724416	0.079	0.389	0
Cox6a2	0	-2.6062141	0.024	0.282	0
H2-D1	0	-0.9365601	0.706	0.941	0
Syngr1	0	-1.4104739	0.482	0.810	0
Cux2	0	1.4455124	0.924	0.821	0
Rps12l1	0	-1.5296697	0.295	0.629	0
Rps13-ps2	0	-2.1192775	0.098	0.410	0
Rps2	0	-1.0391815	0.393	0.786	0
Mt1	0	-0.9889788	0.196	0.594	0
Lipe	0	1.5878442	0.935	0.830	0
Ramp1	0	-2.0524426	0.080	0.380	0
Itgax	0	-2.8686871	0.033	0.286	0
Pld3	0	-1.5493614	0.199	0.557	0
Csf1	0	-2.5105916	0.040	0.301	0
Rplp0	0	-0.9805014	0.543	0.852	0
Rps16	0	-0.9344615	0.444	0.817	0
Atp6v0c	0	-1.0388843	0.507	0.838	0
Psat1	0	-1.5343347	0.048	0.308	0
Tpi1	0	-1.4365039	0.116	0.441	0
Rps5	0	-1.0254345	0.315	0.679	0
Rpl18a	0	-0.7951908	0.767	0.952	0
Ucp2	0	-1.4129656	0.210	0.555	0
Pax6	0	1.6359616	0.846	0.611	0
Tpd52	0	-1.2310377	0.297	0.633	0
Cadm1	0	-1.1234179	0.297	0.651	0
Rpl41	0	-0.8072862	0.617	0.930	0
Ch25h	0	-5.2138413	0.008	0.201	0
Nceh1	0	-2.4527022	0.068	0.328	0
Cd83	0	-1.2975712	0.279	0.629	0
Igf1	0	-4.3451636	0.101	0.367	0
Rpl21	0	-0.7645073	0.506	0.856	0
Rps18	0	-0.7996990	0.554	0.865	0
Eef1b2	0	-0.7655968	0.262	0.618	0
Rpl19	0	-0.8146156	0.399	0.766	0
Rpsa	0	-1.0583222	0.293	0.629	0
Gusb	0	-1.0060868	0.522	0.793	0
Rbm45	0	1.6865553	0.841	0.594	0
Vmn1r13	0	1.0814302	0.914	0.758	0
Rpl26	0	-0.7333611	0.437	0.803	0
Uba52rt	0	-0.7772868	0.388	0.755	0
Rpl29	0	-0.7505988	0.227	0.561	0
Crlf2	0	-1.4283320	0.071	0.338	0
Rpl10-ps3	0	-1.2431144	0.409	0.718	0
Rps26-ps1	0	-1.6984930	0.135	0.419	0
Hexa	0	-0.9791101	0.662	0.904	0
Ndufa2	0	-0.6319746	0.195	0.541	0
Lamp1	0	-0.8093437	0.680	0.915	0
Aplp2	0	-1.2985348	0.134	0.434	0
Tmem119	0	1.2017092	0.872	0.760	0
Lilrb4b	0	-1.0860176	0.038	0.264	0
Fam20c	0	-3.0711934	0.026	0.227	0
Tpt1-ps3	0	-1.0787850	0.225	0.561	0
Rpl28-ps1	0	-0.3789046	0.159	0.483	0
Rps13	0	-0.5005972	0.295	0.655	0
Serpine2	0	-0.8796995	0.701	0.928	0
Galntl6	0	1.8506210	0.867	0.609	0
Rps25	0	-0.5945093	0.615	0.865	0

Microglia1_vs_Microglia3

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-32.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
C1qc	0	1.0213634	0.959	0.729	0
C1qa	0	0.9620201	0.944	0.675	0
Csf1r	0	0.9534023	0.956	0.759	0
Ctsd	0	0.9241694	0.954	0.793	0
Laptm5	0	0.9943457	0.917	0.665	0
Olfml3	0	1.2178115	0.875	0.586	0
Rab3gap1	0	2.4087082	0.636	0.207	0
Ubb	0	0.8321054	0.824	0.394	0
Serinc3	0	0.6360570	0.946	0.714	0
Psap	0	0.8041872	0.894	0.626	0
Lgmn	0	0.7549278	0.961	0.788	0
Or8b44	0	-4.3679983	0.896	0.921	0
Tmem119	0	0.9274532	0.872	0.576	0
Ppp2r5a	0	1.2131561	0.586	0.182	0
H2-D1	0	1.5052900	0.706	0.355	0
Selplg	0	0.7499584	0.924	0.670	0
Selenop	0	0.6341759	0.852	0.512	0
Serpine2	0	1.6932107	0.701	0.369	0
Man2b1	0	0.8586168	0.742	0.399	0
Rps27	0	0.5457671	0.791	0.360	0
Vmn1r13	0	-3.8768569	0.914	0.946	0
Ctss	0	0.6319094	0.987	0.847	0
Bmp2k	0	0.6160680	0.831	0.468	0
Lpcat2	0	0.6024650	0.809	0.463	0
Pdia3	0	1.0990126	0.675	0.325	0
Trem2	0	0.8274776	0.841	0.527	0
Rsrp1	0	0.8015566	0.800	0.468	0
Ctsb	0	0.6224608	0.876	0.586	0
Cep85	0	1.0971267	0.746	0.360	0
Cd81	0	0.7046374	0.926	0.724	0
Fth1	0	0.5023903	0.847	0.581	0
Ly86	0	0.4876841	0.847	0.512	0
Cx3cr1	0	0.6926145	0.945	0.704	0
Ctsz	0	0.6867657	0.837	0.552	0
Dbf4	0	2.0923392	0.454	0.108	0
Son	0	0.3988073	0.862	0.522	0
Tgfbr1	0	0.3728372	0.886	0.571	0
Noct	0	0.5270758	0.778	0.409	0
Fcgr3	0	0.3950869	0.867	0.567	0
Slc38a6	0	0.5948235	0.718	0.369	0
Pikfyve	0	0.1622974	0.700	0.296	0
Tmem234	0	2.7136153	0.569	0.212	0
Cd9	0	0.9451968	0.800	0.537	0
C1qb	0	0.6719789	0.949	0.749	0
Fyco1	0	1.4604339	0.537	0.182	0
Ifngr1	0	0.2276859	0.801	0.473	0
Dleu2	0	0.6787359	0.710	0.335	0
Chd9	0	0.1334925	0.807	0.433	0
Rnaset2a	0	1.3095067	0.668	0.325	0
Rpl18a	0	0.3416075	0.767	0.389	0
Ctsh	0	0.0247743	0.675	0.379	0
Ftl1	0	0.5053478	0.837	0.517	0
Rhoa	0	0.8140671	0.661	0.315	0
Frmd4a	0	0.6215722	0.636	0.286	0
Jund	0	0.4692998	0.527	0.187	0
Hsp90b1	0	0.4945921	0.662	0.330	0
Ubc	0	1.5295952	0.643	0.330	0
Srrm2	0	0.3832654	0.822	0.483	0
Eif2a	0	-2.9569058	0.937	0.941	0
Tprkb	0	-0.7201418	0.463	0.133	0
Lman2l	0	0.3461597	0.635	0.286	0
Ctsa	0	0.5659041	0.788	0.502	0
Dnajb14	0	1.6227726	0.514	0.177	0
Lair1	0	1.0255420	0.717	0.429	0
Trf	0	0.2244779	0.786	0.488	0
Sirt5	0	1.0384590	0.672	0.330	0
Arhgef40	0	0.5835365	0.612	0.251	0
Bin1	0	0.5626523	0.574	0.227	0
Inpp5d	0	0.4020445	0.690	0.355	0
Sfi1	0	1.6708805	0.617	0.291	0
Upf3a	0	2.0410249	0.537	0.187	0
Unc93b1	0	0.6611136	0.692	0.365	0
Nisch	0	1.6147044	0.675	0.335	0
Rigi	0	3.9273355	0.496	0.177	0
Cyth4	0	1.1341181	0.696	0.389	0
Agl	0	2.6402833	0.487	0.163	0
Pld4	0	1.0602185	0.756	0.498	0
Vps13d	0	2.1403831	0.559	0.217	0
Actb	0	0.4233667	0.987	0.921	0
Scamp2	0	0.7599338	0.588	0.296	0
Tmcc3	0	1.6289870	0.428	0.118	0
Trmt1l	0	0.2015740	0.613	0.236	0
Hexb	0	0.5360910	0.992	0.882	0
mt-Co1	0	0.3127764	0.870	0.567	0
Hspa8	0	0.9055108	0.686	0.374	0
Plxdc2	0	1.4892885	0.656	0.384	0
Tmbim6	0	1.2221333	0.667	0.365	0
Qki	0	0.7493048	0.796	0.453	0
Nrros	0	0.3626514	0.594	0.261	0
Elmo1	0	1.5622476	0.592	0.286	0
H3f3b	0	0.3823258	0.725	0.365	0
Tcf7l2	0	-3.5281143	0.884	0.921	0
Cdc40	0	2.6836665	0.433	0.133	0
Ubb-ps	0	0.3791072	0.795	0.399	0
Pag1	0	1.8918038	0.503	0.192	0
Sft2d1	0	0.5196270	0.642	0.320	0
Rbm39	0	0.4898347	0.753	0.424	0
Cd80	0	2.4457863	0.424	0.118	0
Siglech	0	0.5576991	0.882	0.616	0
Mpeg1	0	0.5858987	0.726	0.404	0

Microglia1_vs_Microglia3_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-35.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
C1qc	0	1.0213634	0.959	0.729	0
C1qa	0	0.9620201	0.944	0.675	0
Csf1r	0	0.9534023	0.956	0.759	0
Ctsd	0	0.9241694	0.954	0.793	0
Laptm5	0	0.9943457	0.917	0.665	0
Olfml3	0	1.2178115	0.875	0.586	0
Rab3gap1	0	2.4087082	0.636	0.207	0
Ubb	0	0.8321054	0.824	0.394	0
Serinc3	0	0.6360570	0.946	0.714	0
Psap	0	0.8041872	0.894	0.626	0
Lgmn	0	0.7549278	0.961	0.788	0
Or8b44	0	-4.3679983	0.896	0.921	0
Tmem119	0	0.9274532	0.872	0.576	0
Ppp2r5a	0	1.2131561	0.586	0.182	0
H2-D1	0	1.5052900	0.706	0.355	0
Selplg	0	0.7499584	0.924	0.670	0
Selenop	0	0.6341759	0.852	0.512	0
Serpine2	0	1.6932107	0.701	0.369	0
Man2b1	0	0.8586168	0.742	0.399	0
Rps27	0	0.5457671	0.791	0.360	0
Vmn1r13	0	-3.8768569	0.914	0.946	0
Ctss	0	0.6319094	0.987	0.847	0
Bmp2k	0	0.6160680	0.831	0.468	0
Lpcat2	0	0.6024650	0.809	0.463	0
Pdia3	0	1.0990126	0.675	0.325	0
Trem2	0	0.8274776	0.841	0.527	0
Rsrp1	0	0.8015566	0.800	0.468	0
Ctsb	0	0.6224608	0.876	0.586	0
Cep85	0	1.0971267	0.746	0.360	0
Cd81	0	0.7046374	0.926	0.724	0
Fth1	0	0.5023903	0.847	0.581	0
Ly86	0	0.4876841	0.847	0.512	0
Cx3cr1	0	0.6926145	0.945	0.704	0
Ctsz	0	0.6867657	0.837	0.552	0
Dbf4	0	2.0923392	0.454	0.108	0
Son	0	0.3988073	0.862	0.522	0
Tgfbr1	0	0.3728372	0.886	0.571	0
Noct	0	0.5270758	0.778	0.409	0
Fcgr3	0	0.3950869	0.867	0.567	0
Slc38a6	0	0.5948235	0.718	0.369	0
Pikfyve	0	0.1622974	0.700	0.296	0
Tmem234	0	2.7136153	0.569	0.212	0
Cd9	0	0.9451968	0.800	0.537	0
C1qb	0	0.6719789	0.949	0.749	0
Fyco1	0	1.4604339	0.537	0.182	0
Ifngr1	0	0.2276859	0.801	0.473	0
Dleu2	0	0.6787359	0.710	0.335	0
Chd9	0	0.1334925	0.807	0.433	0
Rnaset2a	0	1.3095067	0.668	0.325	0
Rpl18a	0	0.3416075	0.767	0.389	0
Ctsh	0	0.0247743	0.675	0.379	0
Ftl1	0	0.5053478	0.837	0.517	0
Rhoa	0	0.8140671	0.661	0.315	0
Frmd4a	0	0.6215722	0.636	0.286	0
Jund	0	0.4692998	0.527	0.187	0
Hsp90b1	0	0.4945921	0.662	0.330	0
Ubc	0	1.5295952	0.643	0.330	0
Srrm2	0	0.3832654	0.822	0.483	0
Eif2a	0	-2.9569058	0.937	0.941	0
Tprkb	0	-0.7201418	0.463	0.133	0
Lman2l	0	0.3461597	0.635	0.286	0
Ctsa	0	0.5659041	0.788	0.502	0
Dnajb14	0	1.6227726	0.514	0.177	0
Lair1	0	1.0255420	0.717	0.429	0
Trf	0	0.2244779	0.786	0.488	0
Sirt5	0	1.0384590	0.672	0.330	0
Arhgef40	0	0.5835365	0.612	0.251	0
Bin1	0	0.5626523	0.574	0.227	0
Inpp5d	0	0.4020445	0.690	0.355	0
Sfi1	0	1.6708805	0.617	0.291	0
Upf3a	0	2.0410249	0.537	0.187	0
Unc93b1	0	0.6611136	0.692	0.365	0
Nisch	0	1.6147044	0.675	0.335	0
Rigi	0	3.9273355	0.496	0.177	0
Cyth4	0	1.1341181	0.696	0.389	0
Agl	0	2.6402833	0.487	0.163	0
Pld4	0	1.0602185	0.756	0.498	0
Vps13d	0	2.1403831	0.559	0.217	0
Actb	0	0.4233667	0.987	0.921	0
Scamp2	0	0.7599338	0.588	0.296	0
Tmcc3	0	1.6289870	0.428	0.118	0
Trmt1l	0	0.2015740	0.613	0.236	0
Hexb	0	0.5360910	0.992	0.882	0
mt-Co1	0	0.3127764	0.870	0.567	0
Hspa8	0	0.9055108	0.686	0.374	0
Plxdc2	0	1.4892885	0.656	0.384	0
Tmbim6	0	1.2221333	0.667	0.365	0
Qki	0	0.7493048	0.796	0.453	0
Nrros	0	0.3626514	0.594	0.261	0
Elmo1	0	1.5622476	0.592	0.286	0
H3f3b	0	0.3823258	0.725	0.365	0
Tcf7l2	0	-3.5281143	0.884	0.921	0
Cdc40	0	2.6836665	0.433	0.133	0
Ubb-ps	0	0.3791072	0.795	0.399	0
Pag1	0	1.8918038	0.503	0.192	0
Sft2d1	0	0.5196270	0.642	0.320	0
Rbm39	0	0.4898347	0.753	0.424	0
Cd80	0	2.4457863	0.424	0.118	0
Siglech	0	0.5576991	0.882	0.616	0
Mpeg1	0	0.5858987	0.726	0.404	0

Microglia1_vs_Microglia4

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Ifit3	0	-7.6836575	0.035	0.628	0e+00
Rtp4	0	-3.4269783	0.093	0.717	0e+00
Ifit2	0	-5.7226144	0.020	0.425	0e+00
Ifi206	0	-5.9016986	0.005	0.319	0e+00
Irf7	0	-5.2595288	0.020	0.398	0e+00
Oas2	0	-6.9393210	0.009	0.327	0e+00
Ccl12	0	-4.0601690	0.134	0.690	0e+00
Ifitm3	0	-4.0940045	0.078	0.566	0e+00
Oas1a	0	-3.7958610	0.039	0.460	0e+00
Oasl2	0	-6.6386633	0.151	0.673	0e+00
Mx1	0	-5.7190001	0.071	0.522	0e+00
Usp18	0	-4.2357222	0.060	0.504	0e+00
Stat1	0	-2.9876200	0.255	0.823	0e+00
Ifi27l2a	0	-3.2639683	0.074	0.540	0e+00
Tgtp2	0	-5.9720180	0.034	0.389	0e+00
Ifi211	0	-6.0183554	0.009	0.283	0e+00
Ifi207	0	-5.7326783	0.025	0.354	0e+00
Ifit3b	0	-8.0293608	0.081	0.504	0e+00
Oas1g	0	-3.4631047	0.039	0.407	0e+00
Nlrc5	0	-2.8635630	0.045	0.425	0e+00
Mx2	0	-4.5855953	0.019	0.310	0e+00
Zbp1	0	-4.9466230	0.035	0.363	0e+00
Lgals3bp	0	-2.5751171	0.315	0.814	0e+00
Rnf213	0	-2.5193816	0.139	0.628	0e+00
Phf11b	0	-3.8510101	0.045	0.389	0e+00
Trim30a	0	-1.9922470	0.230	0.726	0e+00
Ifi209	0	-3.6612821	0.088	0.469	0e+00
Trex1	0	-2.3489345	0.128	0.575	0e+00
Phf11a	0	-5.1883581	0.039	0.345	0e+00
Iigp1	0	-5.3856932	0.141	0.558	0e+00
Ifit1	0	-6.5414183	0.051	0.363	0e+00
Iigp1c	0	-3.4666543	0.189	0.602	0e+00
Fgl2	0	-2.9387304	0.076	0.442	0e+00
Trim30d	0	-2.1350605	0.148	0.584	0e+00
Ifi204	0	-2.9241664	0.307	0.726	0e+00
Helz2	0	-9.1157491	0.008	0.195	0e+00
Parp12	0	-2.4273847	0.075	0.416	0e+00
Rsad2	0	-6.8488297	0.044	0.319	0e+00
Gvin1	0	-2.1665846	0.161	0.593	0e+00
Cmpk2	0	-5.1802465	0.004	0.159	0e+00
Tor3a	0	-1.4478519	0.121	0.496	0e+00
Ifi213	0	-5.6531206	0.156	0.513	0e+00
Slfn2	0	-3.1617971	0.128	0.487	0e+00
Bst2	0	-2.0339628	0.166	0.558	0e+00
Gvin2	0	-2.3457184	0.180	0.593	0e+00
Oasl1	0	-8.3848299	0.010	0.177	0e+00
Samd9l	0	-2.3838732	0.030	0.257	0e+00
Isg15	0	-3.6217003	0.133	0.460	0e+00
Phf11d	0	-2.8198216	0.114	0.442	0e+00
Ifi208	0	-3.6570245	0.130	0.469	0e+00
Slfn8	0	-1.8602422	0.267	0.673	0e+00
Parp9	0	-2.2835738	0.085	0.389	0e+00
Ifi214	0	-3.2801761	0.123	0.451	0e+00
Parp14	0	-2.7384079	0.196	0.531	0e+00
Ifi205	0	-4.1872323	0.010	0.159	0e+00
Sp100	0	-2.8012144	0.287	0.611	0e+00
Herc6	0	-2.6516256	0.358	0.681	0e+00
Gvin-ps7	0	-2.2710598	0.207	0.558	0e+00
Xaf1	0	-2.4885923	0.406	0.708	0e+00
Psmb8	0	-1.4728430	0.308	0.690	0e+00
Ly6a	0	-2.7870305	0.024	0.204	0e+00
Etnk1	0	-1.5101625	0.218	0.575	0e+00
Fcgr1	0	-1.1017639	0.477	0.850	0e+00
Axl	0	-2.5188740	0.073	0.327	0e+00
Irgm1	0	-2.5222329	0.234	0.549	0e+00
Ifih1	0	-1.8123811	0.103	0.381	0e+00
Nampt	0	-2.3772952	0.056	0.283	0e+00
Ly6e	0	-1.2520987	0.680	0.912	0e+00
Ifi35	0	-1.5997760	0.116	0.416	0e+00
Gbp9	0	-1.4750605	0.056	0.283	0e+00
Slfn5	0	-2.1892455	0.421	0.717	0e+00
Znfx1	0	-1.6048796	0.194	0.522	0e+00
Ddx60	0	-1.8121202	0.109	0.381	0e+00
B2m	0	-0.6923878	0.949	1.000	0e+00
Isg20	0	-1.5801535	0.028	0.195	0e+00
Dhx58	0	-3.0240630	0.134	0.398	0e+00
Dtx3l	0	-1.5922911	0.363	0.690	0e+00
Sdc3	0	-2.3546565	0.069	0.292	0e+00
Ifi47	0	-6.8057973	0.004	0.097	0e+00
Epsti1	0	-1.6691286	0.089	0.336	0e+00
Eif2ak2	0	-1.1031130	0.494	0.779	0e+00
Trafd1	0	-1.5215331	0.190	0.496	0e+00
Trem6l	0	-2.3008212	0.099	0.336	0e+00
Tap1	0	-1.7399457	0.106	0.354	0e+00
Scimp	0	-3.1149380	0.015	0.142	0e+00
Ccl2	0	-4.3079631	0.015	0.142	0e+00
Sp110	0	-1.3571338	0.217	0.513	0e+00
Pml	0	-2.1044100	0.106	0.336	0e+00
Adar	0	-0.9879565	0.089	0.319	0e+00
Cst7	0	-3.0200531	0.089	0.310	0e+00
Nmi	0	-1.2919726	0.074	0.292	0e+00
Phf11	0	-1.5011940	0.008	0.106	0e+00
H2-D1	0	-0.9590311	0.706	0.903	0e+00
Oas1b	0	-1.8027668	0.060	0.257	0e+00
Trim30c	0	-3.5829729	0.006	0.097	1e-07
H2-Q6	0	-2.6144165	0.217	0.487	1e-07
Cd52	0	-1.0951126	0.292	0.628	2e-07
Psme2b	0	-1.6675677	0.170	0.442	2e-07
Ogfr	0	-1.6458533	0.074	0.274	3e-07
Marchf5	0	-1.9246377	0.053	0.230	4e-07

Microglia1_vs_Microglia4_comorbid

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Ifit3	0	-7.6836575	0.035	0.628	0e+00
Rtp4	0	-3.4269783	0.093	0.717	0e+00
Ifit2	0	-5.7226144	0.020	0.425	0e+00
Ifi206	0	-5.9016986	0.005	0.319	0e+00
Irf7	0	-5.2595288	0.020	0.398	0e+00
Oas2	0	-6.9393210	0.009	0.327	0e+00
Ccl12	0	-4.0601690	0.134	0.690	0e+00
Ifitm3	0	-4.0940045	0.078	0.566	0e+00
Oas1a	0	-3.7958610	0.039	0.460	0e+00
Oasl2	0	-6.6386633	0.151	0.673	0e+00
Mx1	0	-5.7190001	0.071	0.522	0e+00
Usp18	0	-4.2357222	0.060	0.504	0e+00
Stat1	0	-2.9876200	0.255	0.823	0e+00
Ifi27l2a	0	-3.2639683	0.074	0.540	0e+00
Tgtp2	0	-5.9720180	0.034	0.389	0e+00
Ifi211	0	-6.0183554	0.009	0.283	0e+00
Ifi207	0	-5.7326783	0.025	0.354	0e+00
Ifit3b	0	-8.0293608	0.081	0.504	0e+00
Oas1g	0	-3.4631047	0.039	0.407	0e+00
Nlrc5	0	-2.8635630	0.045	0.425	0e+00
Mx2	0	-4.5855953	0.019	0.310	0e+00
Zbp1	0	-4.9466230	0.035	0.363	0e+00
Lgals3bp	0	-2.5751171	0.315	0.814	0e+00
Rnf213	0	-2.5193816	0.139	0.628	0e+00
Phf11b	0	-3.8510101	0.045	0.389	0e+00
Trim30a	0	-1.9922470	0.230	0.726	0e+00
Ifi209	0	-3.6612821	0.088	0.469	0e+00
Trex1	0	-2.3489345	0.128	0.575	0e+00
Phf11a	0	-5.1883581	0.039	0.345	0e+00
Iigp1	0	-5.3856932	0.141	0.558	0e+00
Ifit1	0	-6.5414183	0.051	0.363	0e+00
Iigp1c	0	-3.4666543	0.189	0.602	0e+00
Fgl2	0	-2.9387304	0.076	0.442	0e+00
Trim30d	0	-2.1350605	0.148	0.584	0e+00
Ifi204	0	-2.9241664	0.307	0.726	0e+00
Helz2	0	-9.1157491	0.008	0.195	0e+00
Parp12	0	-2.4273847	0.075	0.416	0e+00
Rsad2	0	-6.8488297	0.044	0.319	0e+00
Gvin1	0	-2.1665846	0.161	0.593	0e+00
Cmpk2	0	-5.1802465	0.004	0.159	0e+00
Tor3a	0	-1.4478519	0.121	0.496	0e+00
Ifi213	0	-5.6531206	0.156	0.513	0e+00
Slfn2	0	-3.1617971	0.128	0.487	0e+00
Bst2	0	-2.0339628	0.166	0.558	0e+00
Gvin2	0	-2.3457184	0.180	0.593	0e+00
Oasl1	0	-8.3848299	0.010	0.177	0e+00
Samd9l	0	-2.3838732	0.030	0.257	0e+00
Isg15	0	-3.6217003	0.133	0.460	0e+00
Phf11d	0	-2.8198216	0.114	0.442	0e+00
Ifi208	0	-3.6570245	0.130	0.469	0e+00
Slfn8	0	-1.8602422	0.267	0.673	0e+00
Parp9	0	-2.2835738	0.085	0.389	0e+00
Ifi214	0	-3.2801761	0.123	0.451	0e+00
Parp14	0	-2.7384079	0.196	0.531	0e+00
Ifi205	0	-4.1872323	0.010	0.159	0e+00
Sp100	0	-2.8012144	0.287	0.611	0e+00
Herc6	0	-2.6516256	0.358	0.681	0e+00
Gvin-ps7	0	-2.2710598	0.207	0.558	0e+00
Xaf1	0	-2.4885923	0.406	0.708	0e+00
Psmb8	0	-1.4728430	0.308	0.690	0e+00
Ly6a	0	-2.7870305	0.024	0.204	0e+00
Etnk1	0	-1.5101625	0.218	0.575	0e+00
Fcgr1	0	-1.1017639	0.477	0.850	0e+00
Axl	0	-2.5188740	0.073	0.327	0e+00
Irgm1	0	-2.5222329	0.234	0.549	0e+00
Ifih1	0	-1.8123811	0.103	0.381	0e+00
Nampt	0	-2.3772952	0.056	0.283	0e+00
Ly6e	0	-1.2520987	0.680	0.912	0e+00
Ifi35	0	-1.5997760	0.116	0.416	0e+00
Gbp9	0	-1.4750605	0.056	0.283	0e+00
Slfn5	0	-2.1892455	0.421	0.717	0e+00
Znfx1	0	-1.6048796	0.194	0.522	0e+00
Ddx60	0	-1.8121202	0.109	0.381	0e+00
B2m	0	-0.6923878	0.949	1.000	0e+00
Isg20	0	-1.5801535	0.028	0.195	0e+00
Dhx58	0	-3.0240630	0.134	0.398	0e+00
Dtx3l	0	-1.5922911	0.363	0.690	0e+00
Sdc3	0	-2.3546565	0.069	0.292	0e+00
Ifi47	0	-6.8057973	0.004	0.097	0e+00
Epsti1	0	-1.6691286	0.089	0.336	0e+00
Eif2ak2	0	-1.1031130	0.494	0.779	0e+00
Trafd1	0	-1.5215331	0.190	0.496	0e+00
Trem6l	0	-2.3008212	0.099	0.336	0e+00
Tap1	0	-1.7399457	0.106	0.354	0e+00
Scimp	0	-3.1149380	0.015	0.142	0e+00
Ccl2	0	-4.3079631	0.015	0.142	0e+00
Sp110	0	-1.3571338	0.217	0.513	0e+00
Pml	0	-2.1044100	0.106	0.336	0e+00
Adar	0	-0.9879565	0.089	0.319	0e+00
Cst7	0	-3.0200531	0.089	0.310	0e+00
Nmi	0	-1.2919726	0.074	0.292	0e+00
Phf11	0	-1.5011940	0.008	0.106	0e+00
H2-D1	0	-0.9590311	0.706	0.903	0e+00
Oas1b	0	-1.8027668	0.060	0.257	0e+00
Trim30c	0	-3.5829729	0.006	0.097	1e-07
H2-Q6	0	-2.6144165	0.217	0.487	1e-07
Cd52	0	-1.0951126	0.292	0.628	2e-07
Psme2b	0	-1.6675677	0.170	0.442	2e-07
Ogfr	0	-1.6458533	0.074	0.274	3e-07
Marchf5	0	-1.9246377	0.053	0.230	4e-07

Microglia1_vs_Microglia5

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0e+00	-9.1615935	0.026	0.904	0.0000000
Cd74	0.0e+00	-7.2748897	0.096	0.959	0.0000000
H2-Eb1	0.0e+00	-9.5285827	0.021	0.630	0.0000000
H2-Aa	0.0e+00	-10.3520212	0.071	0.712	0.0000000
H2-D1	0.0e+00	-1.9011179	0.706	0.959	0.0000000
H2-K1	0.0e+00	-1.3779921	0.657	0.932	0.0000000
Usp12	0.0e+00	-1.9021436	0.105	0.425	0.0000000
H2-Oa	0.0e+00	-2.1263695	0.076	0.356	0.0000000
Nbl1	0.0e+00	-8.9196769	0.003	0.096	0.0000000
Wfdc17	0.0e+00	-6.3884755	0.003	0.096	0.0000000
Pfkm	0.0e+00	-3.3132871	0.001	0.082	0.0000000
Ccl3	0.0e+00	-1.3450746	0.048	0.260	0.0000000
Trac	0.0e+00	2.2298370	0.869	0.644	0.0000001
Itgax	0.0e+00	-2.6567752	0.033	0.205	0.0000003
Vwa3b	0.0e+00	-3.8470492	0.001	0.068	0.0000005
H2-Q7	0.0e+00	-3.2320335	0.310	0.603	0.0000008
Arfgef3	0.0e+00	1.5602380	0.874	0.658	0.0000009
Axl	0.0e+00	-1.9759252	0.073	0.301	0.0000012
Capg	0.0e+00	-2.5076612	0.063	0.274	0.0000016
Ccl6	0.0e+00	-1.9626530	0.194	0.507	0.0000031
Ank	0.0e+00	-2.8611782	0.066	0.274	0.0000031
Eif2a	0.0e+00	1.5886406	0.937	0.808	0.0000037
Baiap2l2	0.0e+00	-5.5464903	0.006	0.096	0.0000042
Tspo	0.0e+00	-1.1561638	0.118	0.397	0.0000045
Tsc22d1	0.0e+00	-4.0387725	0.016	0.137	0.0000097
Cst7	0.0e+00	-4.2240302	0.089	0.301	0.0000102
Cox6a2	0.0e+00	-1.7035712	0.024	0.164	0.0000110
Pax6	0.0e+00	1.6032731	0.846	0.671	0.0000178
H2-Q6	0.0e+00	-3.1471948	0.217	0.493	0.0000195
Ifi27l2a	0.0e+00	-1.5391876	0.074	0.288	0.0000257
H2-T23	0.0e+00	-1.3357062	0.526	0.808	0.0000321
Cep290	0.0e+00	1.5055324	0.916	0.712	0.0000341
Hpse	0.0e+00	-8.4965199	0.005	0.082	0.0000413
Clec7a	0.0e+00	-2.5944974	0.081	0.288	0.0000602
B2m	0.0e+00	-0.7872743	0.949	0.986	0.0000660
Or52m1	0.0e+00	2.1355512	0.807	0.575	0.0000800
Ift20	0.0e+00	1.2946543	0.872	0.726	0.0000819
Vmn1r13	0.0e+00	1.4517681	0.914	0.726	0.0000819
Atp1a3	0.0e+00	-2.6780174	0.069	0.260	0.0000824
Colec10	0.0e+00	-5.2619825	0.001	0.055	0.0001118
Vmn1r-ps73	0.0e+00	-1.3940162	0.001	0.055	0.0001143
Ramp1	0.0e+00	-1.3997755	0.080	0.288	0.0001263
Mtss1	0.0e+00	1.4701886	0.756	0.507	0.0001304
Ly6e	0.0e+00	-1.1252784	0.680	0.863	0.0001475
Lancl2	0.0e+00	-7.3231896	0.000	0.041	0.0001560
Prr15	0.0e+00	3.8659262	0.837	0.616	0.0001726
AI593442	0.0e+00	1.6821530	0.747	0.466	0.0002149
Ctsd	0.0e+00	-0.8894259	0.954	0.973	0.0002761
Syngr1	0.0e+00	-1.0531995	0.482	0.753	0.0003254
H2-M3	0.0e+00	-1.3301784	0.153	0.411	0.0003446
Rps16-ps2	0.0e+00	-0.9725873	0.255	0.575	0.0004555
Fgl2	0.0e+00	-1.6657788	0.076	0.274	0.0005406
Lipe	1.0e-07	1.4223459	0.935	0.836	0.0010270
Taf6l	1.0e-07	-1.6705182	0.048	0.205	0.0011975
Cux2	1.0e-07	1.3261330	0.924	0.795	0.0013095
Malat1	1.0e-07	0.5731738	0.987	0.973	0.0016188
Bphl	1.0e-07	-2.5480556	0.028	0.151	0.0020212
Tyrobp	1.0e-07	-1.1456426	0.815	0.973	0.0023687
Spp1	2.0e-07	-7.3747631	0.015	0.110	0.0027070
Pgrmc2	2.0e-07	-1.7936901	0.039	0.178	0.0035689
Dcstamp	2.0e-07	-4.6882512	0.003	0.055	0.0036220
Lrrc8b	2.0e-07	-1.9467945	0.003	0.055	0.0037559
Stx7	2.0e-07	-0.8949923	0.419	0.712	0.0038344
Dido1	3.0e-07	0.8936436	0.907	0.712	0.0039928
Oc90	3.0e-07	-3.0472587	0.003	0.055	0.0040382
Lgals3bp	3.0e-07	-1.7109838	0.315	0.548	0.0047205
Dpf1	3.0e-07	1.3786950	0.682	0.452	0.0052532
Mif	4.0e-07	-1.0478043	0.149	0.384	0.0056331
Slc2a1	4.0e-07	-2.3835466	0.066	0.233	0.0059094
Ctsb	4.0e-07	-0.9025466	0.876	0.959	0.0069171
Slc25a4	5.0e-07	-0.6885710	0.164	0.411	0.0073550
Sem1	5.0e-07	-0.5658439	0.168	0.425	0.0077894
AW112010	6.0e-07	-1.5070601	0.066	0.233	0.0088998
Or8b44	7.0e-07	2.7349923	0.896	0.726	0.0104745
Tmsb10	7.0e-07	-0.2382261	0.194	0.466	0.0107471
Dnajc12	7.0e-07	-1.2350834	0.280	0.534	0.0109490
Il3ra	8.0e-07	-2.2883458	0.009	0.082	0.0120258
Selenom	8.0e-07	-2.8357614	0.009	0.082	0.0123148
Stt3b	8.0e-07	-1.1627459	0.080	0.260	0.0128357
Amy1	8.0e-07	-1.9939308	0.009	0.082	0.0129128
Lratd1	9.0e-07	2.1995711	0.597	0.329	0.0136850
Or14c41	9.0e-07	0.8980247	0.804	0.575	0.0139532
H2-DMa	9.0e-07	-0.9792104	0.323	0.589	0.0148482
Ifi35	1.1e-06	-0.8686203	0.116	0.329	0.0175605
Parp12	1.2e-06	-0.7657879	0.075	0.247	0.0191328
Tmem229b	1.2e-06	-3.3582690	0.079	0.247	0.0194981
Zbtb44	1.3e-06	1.6966785	0.889	0.644	0.0209893
Ly86	1.3e-06	-0.5742444	0.847	0.986	0.0213224
Mamdc2	1.4e-06	-5.5439934	0.001	0.041	0.0224555
Klf2	1.4e-06	-5.9602405	0.001	0.041	0.0224555
Rpl36a-ps2	1.4e-06	-0.4064255	0.163	0.384	0.0230264
Mn1	1.5e-06	1.5169760	0.586	0.329	0.0231627
Cfap221	1.5e-06	-3.7805722	0.001	0.041	0.0234089
Gpx4	1.5e-06	-0.8000959	0.200	0.466	0.0234724
Egln3	1.6e-06	-4.6957650	0.006	0.068	0.0257964
Tap1	1.6e-06	-1.0804145	0.106	0.301	0.0260712
Setd6	1.8e-06	-2.5829705	0.006	0.068	0.0279082
Cd200r4	1.8e-06	-1.5822023	0.006	0.068	0.0286483
Chst12	1.9e-06	-0.9974524	0.069	0.233	0.0308791
Rpl14-ps1	2.4e-06	-1.3172338	0.074	0.233	0.0388496

Microglia1_vs_Microglia5_comorbid

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0e+00	-9.1615935	0.026	0.904	0.0000000
Cd74	0.0e+00	-7.2748897	0.096	0.959	0.0000000
H2-Eb1	0.0e+00	-9.5285827	0.021	0.630	0.0000000
H2-Aa	0.0e+00	-10.3520212	0.071	0.712	0.0000000
H2-D1	0.0e+00	-1.9011179	0.706	0.959	0.0000000
H2-K1	0.0e+00	-1.3779921	0.657	0.932	0.0000000
Usp12	0.0e+00	-1.9021436	0.105	0.425	0.0000000
H2-Oa	0.0e+00	-2.1263695	0.076	0.356	0.0000000
Nbl1	0.0e+00	-8.9196769	0.003	0.096	0.0000000
Wfdc17	0.0e+00	-6.3884755	0.003	0.096	0.0000000
Pfkm	0.0e+00	-3.3132871	0.001	0.082	0.0000000
Ccl3	0.0e+00	-1.3450746	0.048	0.260	0.0000000
Trac	0.0e+00	2.2298370	0.869	0.644	0.0000001
Itgax	0.0e+00	-2.6567752	0.033	0.205	0.0000003
Vwa3b	0.0e+00	-3.8470492	0.001	0.068	0.0000005
H2-Q7	0.0e+00	-3.2320335	0.310	0.603	0.0000008
Arfgef3	0.0e+00	1.5602380	0.874	0.658	0.0000009
Axl	0.0e+00	-1.9759252	0.073	0.301	0.0000012
Capg	0.0e+00	-2.5076612	0.063	0.274	0.0000016
Ccl6	0.0e+00	-1.9626530	0.194	0.507	0.0000031
Ank	0.0e+00	-2.8611782	0.066	0.274	0.0000031
Eif2a	0.0e+00	1.5886406	0.937	0.808	0.0000037
Baiap2l2	0.0e+00	-5.5464903	0.006	0.096	0.0000042
Tspo	0.0e+00	-1.1561638	0.118	0.397	0.0000045
Tsc22d1	0.0e+00	-4.0387725	0.016	0.137	0.0000097
Cst7	0.0e+00	-4.2240302	0.089	0.301	0.0000102
Cox6a2	0.0e+00	-1.7035712	0.024	0.164	0.0000110
Pax6	0.0e+00	1.6032731	0.846	0.671	0.0000178
H2-Q6	0.0e+00	-3.1471948	0.217	0.493	0.0000195
Ifi27l2a	0.0e+00	-1.5391876	0.074	0.288	0.0000257
H2-T23	0.0e+00	-1.3357062	0.526	0.808	0.0000321
Cep290	0.0e+00	1.5055324	0.916	0.712	0.0000341
Hpse	0.0e+00	-8.4965199	0.005	0.082	0.0000413
Clec7a	0.0e+00	-2.5944974	0.081	0.288	0.0000602
B2m	0.0e+00	-0.7872743	0.949	0.986	0.0000660
Or52m1	0.0e+00	2.1355512	0.807	0.575	0.0000800
Ift20	0.0e+00	1.2946543	0.872	0.726	0.0000819
Vmn1r13	0.0e+00	1.4517681	0.914	0.726	0.0000819
Atp1a3	0.0e+00	-2.6780174	0.069	0.260	0.0000824
Colec10	0.0e+00	-5.2619825	0.001	0.055	0.0001118
Vmn1r-ps73	0.0e+00	-1.3940162	0.001	0.055	0.0001143
Ramp1	0.0e+00	-1.3997755	0.080	0.288	0.0001263
Mtss1	0.0e+00	1.4701886	0.756	0.507	0.0001304
Ly6e	0.0e+00	-1.1252784	0.680	0.863	0.0001475
Lancl2	0.0e+00	-7.3231896	0.000	0.041	0.0001560
Prr15	0.0e+00	3.8659262	0.837	0.616	0.0001726
AI593442	0.0e+00	1.6821530	0.747	0.466	0.0002149
Ctsd	0.0e+00	-0.8894259	0.954	0.973	0.0002761
Syngr1	0.0e+00	-1.0531995	0.482	0.753	0.0003254
H2-M3	0.0e+00	-1.3301784	0.153	0.411	0.0003446
Rps16-ps2	0.0e+00	-0.9725873	0.255	0.575	0.0004555
Fgl2	0.0e+00	-1.6657788	0.076	0.274	0.0005406
Lipe	1.0e-07	1.4223459	0.935	0.836	0.0010270
Taf6l	1.0e-07	-1.6705182	0.048	0.205	0.0011975
Cux2	1.0e-07	1.3261330	0.924	0.795	0.0013095
Malat1	1.0e-07	0.5731738	0.987	0.973	0.0016188
Bphl	1.0e-07	-2.5480556	0.028	0.151	0.0020212
Tyrobp	1.0e-07	-1.1456426	0.815	0.973	0.0023687
Spp1	2.0e-07	-7.3747631	0.015	0.110	0.0027070
Pgrmc2	2.0e-07	-1.7936901	0.039	0.178	0.0035689
Dcstamp	2.0e-07	-4.6882512	0.003	0.055	0.0036220
Lrrc8b	2.0e-07	-1.9467945	0.003	0.055	0.0037559
Stx7	2.0e-07	-0.8949923	0.419	0.712	0.0038344
Dido1	3.0e-07	0.8936436	0.907	0.712	0.0039928
Oc90	3.0e-07	-3.0472587	0.003	0.055	0.0040382
Lgals3bp	3.0e-07	-1.7109838	0.315	0.548	0.0047205
Dpf1	3.0e-07	1.3786950	0.682	0.452	0.0052532
Mif	4.0e-07	-1.0478043	0.149	0.384	0.0056331
Slc2a1	4.0e-07	-2.3835466	0.066	0.233	0.0059094
Ctsb	4.0e-07	-0.9025466	0.876	0.959	0.0069171
Slc25a4	5.0e-07	-0.6885710	0.164	0.411	0.0073550
Sem1	5.0e-07	-0.5658439	0.168	0.425	0.0077894
AW112010	6.0e-07	-1.5070601	0.066	0.233	0.0088998
Or8b44	7.0e-07	2.7349923	0.896	0.726	0.0104745
Tmsb10	7.0e-07	-0.2382261	0.194	0.466	0.0107471
Dnajc12	7.0e-07	-1.2350834	0.280	0.534	0.0109490
Il3ra	8.0e-07	-2.2883458	0.009	0.082	0.0120258
Selenom	8.0e-07	-2.8357614	0.009	0.082	0.0123148
Stt3b	8.0e-07	-1.1627459	0.080	0.260	0.0128357
Amy1	8.0e-07	-1.9939308	0.009	0.082	0.0129128
Lratd1	9.0e-07	2.1995711	0.597	0.329	0.0136850
Or14c41	9.0e-07	0.8980247	0.804	0.575	0.0139532
H2-DMa	9.0e-07	-0.9792104	0.323	0.589	0.0148482
Ifi35	1.1e-06	-0.8686203	0.116	0.329	0.0175605
Parp12	1.2e-06	-0.7657879	0.075	0.247	0.0191328
Tmem229b	1.2e-06	-3.3582690	0.079	0.247	0.0194981
Zbtb44	1.3e-06	1.6966785	0.889	0.644	0.0209893
Ly86	1.3e-06	-0.5742444	0.847	0.986	0.0213224
Mamdc2	1.4e-06	-5.5439934	0.001	0.041	0.0224555
Klf2	1.4e-06	-5.9602405	0.001	0.041	0.0224555
Rpl36a-ps2	1.4e-06	-0.4064255	0.163	0.384	0.0230264
Mn1	1.5e-06	1.5169760	0.586	0.329	0.0231627
Cfap221	1.5e-06	-3.7805722	0.001	0.041	0.0234089
Gpx4	1.5e-06	-0.8000959	0.200	0.466	0.0234724
Egln3	1.6e-06	-4.6957650	0.006	0.068	0.0257964
Tap1	1.6e-06	-1.0804145	0.106	0.301	0.0260712
Setd6	1.8e-06	-2.5829705	0.006	0.068	0.0279082
Cd200r4	1.8e-06	-1.5822023	0.006	0.068	0.0286483
Chst12	1.9e-06	-0.9974524	0.069	0.233	0.0308791
Rpl14-ps1	2.4e-06	-1.3172338	0.074	0.233	0.0388496

Microglia2_vs_Microglia3

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-46.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Apoe	0	3.9199970	0.937	0.374	0
Ctsd	0	2.2925635	1.000	0.793	0
Ctsb	0	2.1141633	0.993	0.586	0
Ctsz	0	2.0452690	0.987	0.552	0
Lyz2	0	2.4068165	0.921	0.320	0
H2-D1	0	2.4418500	0.941	0.355	0
Cd9	0	2.0479351	0.969	0.537	0
Serpine2	0	2.5729102	0.928	0.369	0
Fth1	0	1.6678635	0.983	0.581	0
Tyrobp	0	2.1800743	0.980	0.562	0
Ftl1	0	1.7163234	0.976	0.517	0
Cst7	0	6.7126878	0.705	0.074	0
Cd63	0	1.9262651	0.893	0.281	0
Rps2	0	2.5952528	0.786	0.128	0
Cd68	0	1.2503386	0.932	0.399	0
Lgals3bp	0	3.3596085	0.758	0.158	0
Clec7a	0	2.5519793	0.668	0.054	0
Ctsa	0	1.2311744	0.959	0.502	0
Uba52	0	0.1121277	0.812	0.167	0
Vmn1r13	0	-4.9582871	0.758	0.946	0
Syngr1	0	2.6954257	0.810	0.256	0
Rpl18a	0	1.1367984	0.952	0.389	0
Trem2	0	1.4883107	0.963	0.527	0
Lpl	0	4.1970190	0.825	0.271	0
Or8b44	0	-6.4928759	0.707	0.921	0
Atp6v0c	0	1.7958977	0.838	0.296	0
Lipe	0	-4.3434442	0.830	0.975	0
H2-K1	0	1.7550056	0.900	0.389	0
Uba52rt	0	0.1782772	0.755	0.153	0
Npc2	0	1.1769112	0.926	0.429	0
Hexa	0	1.4214090	0.904	0.409	0
Grn	0	1.4039361	0.945	0.473	0
Ctsl	0	1.2654097	0.969	0.591	0
Rpl41	0	0.1334857	0.930	0.330	0
Tpt1	0	1.7310788	0.825	0.276	0
Ly86	0	1.0423897	0.965	0.512	0
Gusb	0	1.4721025	0.793	0.271	0
Gapdh	0	0.1362397	0.841	0.320	0
Rplp0	0	1.6586937	0.852	0.315	0
Ctsh	0	0.2664088	0.893	0.379	0
Aldoa	0	2.2642062	0.784	0.246	0
Eef1a1	0	0.8877638	0.989	0.660	0
Hspa8	0	1.2737738	0.900	0.374	0
C1qc	0	1.2484864	0.996	0.729	0
C1qa	0	1.2736360	0.998	0.675	0
Rps24	0	0.2889303	0.865	0.261	0
Mif	0	3.7970152	0.605	0.054	0
Trac	0	-5.3396713	0.568	0.823	0
Mpeg1	0	1.1410246	0.924	0.404	0
Sh3bgrl3	0	1.3232246	0.745	0.167	0
Rps9	0	1.0530632	0.884	0.335	0
Rps19	0	0.7872978	0.871	0.310	0
Rps16-ps2	0	2.3027221	0.701	0.128	0
Pkm	0	2.2779373	0.642	0.094	0
Eif2a	0	-3.9020174	0.858	0.941	0
Serf2	0	0.8183050	0.784	0.182	0
Rpl13a	0	1.0232587	0.917	0.355	0
Axl	0	8.9220958	0.533	0.020	0
Rplp1	0	0.5833906	0.932	0.389	0
Rps5	0	1.8679160	0.679	0.133	0
Cux2	0	-4.2456520	0.821	0.906	0
Prdx1	0	1.0066697	0.755	0.227	0
Plxdc2	0	1.6362229	0.843	0.384	0
Rps18	0	1.0258005	0.865	0.300	0
Cfl1	0	1.2196355	0.884	0.463	0
Man2b1	0	0.9932871	0.886	0.399	0
Cd52	0	0.6197818	0.738	0.187	0
Rps6	0	0.7430137	0.779	0.197	0
Rpl19	0	1.2497134	0.766	0.182	0
Cox4i1	0	1.3180256	0.795	0.227	0
Arfgef3	0	-4.0098038	0.574	0.833	0
Rps23-ps1	0	1.1017877	0.841	0.246	0
Rps16	0	0.9529365	0.817	0.246	0
Rplp2	0	0.7315401	0.793	0.207	0
AU020206	0	2.4513427	0.688	0.172	0
Rps28	0	1.0094138	0.891	0.291	0
Laptm5	0	1.2047213	0.969	0.665	0
Rpl3	0	1.4624131	0.773	0.232	0
Ppt1	0	1.4212335	0.749	0.246	0
Lamp1	0	0.4694796	0.915	0.448	0
Creg1	0	0.9666021	0.773	0.251	0
B2m	0	0.9439195	0.989	0.734	0
Hif1a	0	3.1804196	0.587	0.074	0
Rpl15	0	0.8104652	0.749	0.182	0
Rpl13	0	0.7091759	0.880	0.305	0
Rpl35a	0	0.5728594	0.736	0.172	0
Cd83	0	3.1097143	0.629	0.128	0
Rpl32	0	0.0061385	0.882	0.305	0
Rbm45	0	-5.0699120	0.594	0.828	0
Hsp90b1	0	0.6376631	0.841	0.330	0
Pdia3	0	1.0331859	0.828	0.325	0
Rps8	0	1.5908680	0.714	0.187	0
Ctss	0	0.9543452	1.000	0.847	0
Ccl3	0	4.4857741	0.533	0.044	0
Dnajb14	0	2.3303873	0.692	0.177	0
Cadm1	0	1.7429086	0.651	0.143	0
Gnas	0	1.7107747	0.734	0.212	0
Rpl10a	0	0.2706754	0.801	0.261	0
Psap	0	0.9238396	0.985	0.626	0
Rpl18	0	0.7048072	0.740	0.207	0

Microglia2_vs_Microglia3_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-49.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Apoe	0	3.9199970	0.937	0.374	0
Ctsd	0	2.2925635	1.000	0.793	0
Ctsb	0	2.1141633	0.993	0.586	0
Ctsz	0	2.0452690	0.987	0.552	0
Lyz2	0	2.4068165	0.921	0.320	0
H2-D1	0	2.4418500	0.941	0.355	0
Cd9	0	2.0479351	0.969	0.537	0
Serpine2	0	2.5729102	0.928	0.369	0
Fth1	0	1.6678635	0.983	0.581	0
Tyrobp	0	2.1800743	0.980	0.562	0
Ftl1	0	1.7163234	0.976	0.517	0
Cst7	0	6.7126878	0.705	0.074	0
Cd63	0	1.9262651	0.893	0.281	0
Rps2	0	2.5952528	0.786	0.128	0
Cd68	0	1.2503386	0.932	0.399	0
Lgals3bp	0	3.3596085	0.758	0.158	0
Clec7a	0	2.5519793	0.668	0.054	0
Ctsa	0	1.2311744	0.959	0.502	0
Uba52	0	0.1121277	0.812	0.167	0
Vmn1r13	0	-4.9582871	0.758	0.946	0
Syngr1	0	2.6954257	0.810	0.256	0
Rpl18a	0	1.1367984	0.952	0.389	0
Trem2	0	1.4883107	0.963	0.527	0
Lpl	0	4.1970190	0.825	0.271	0
Or8b44	0	-6.4928759	0.707	0.921	0
Atp6v0c	0	1.7958977	0.838	0.296	0
Lipe	0	-4.3434442	0.830	0.975	0
H2-K1	0	1.7550056	0.900	0.389	0
Uba52rt	0	0.1782772	0.755	0.153	0
Npc2	0	1.1769112	0.926	0.429	0
Hexa	0	1.4214090	0.904	0.409	0
Grn	0	1.4039361	0.945	0.473	0
Ctsl	0	1.2654097	0.969	0.591	0
Rpl41	0	0.1334857	0.930	0.330	0
Tpt1	0	1.7310788	0.825	0.276	0
Ly86	0	1.0423897	0.965	0.512	0
Gusb	0	1.4721025	0.793	0.271	0
Gapdh	0	0.1362397	0.841	0.320	0
Rplp0	0	1.6586937	0.852	0.315	0
Ctsh	0	0.2664088	0.893	0.379	0
Aldoa	0	2.2642062	0.784	0.246	0
Eef1a1	0	0.8877638	0.989	0.660	0
Hspa8	0	1.2737738	0.900	0.374	0
C1qc	0	1.2484864	0.996	0.729	0
C1qa	0	1.2736360	0.998	0.675	0
Rps24	0	0.2889303	0.865	0.261	0
Mif	0	3.7970152	0.605	0.054	0
Trac	0	-5.3396713	0.568	0.823	0
Mpeg1	0	1.1410246	0.924	0.404	0
Sh3bgrl3	0	1.3232246	0.745	0.167	0
Rps9	0	1.0530632	0.884	0.335	0
Rps19	0	0.7872978	0.871	0.310	0
Rps16-ps2	0	2.3027221	0.701	0.128	0
Pkm	0	2.2779373	0.642	0.094	0
Eif2a	0	-3.9020174	0.858	0.941	0
Serf2	0	0.8183050	0.784	0.182	0
Rpl13a	0	1.0232587	0.917	0.355	0
Axl	0	8.9220958	0.533	0.020	0
Rplp1	0	0.5833906	0.932	0.389	0
Rps5	0	1.8679160	0.679	0.133	0
Cux2	0	-4.2456520	0.821	0.906	0
Prdx1	0	1.0066697	0.755	0.227	0
Plxdc2	0	1.6362229	0.843	0.384	0
Rps18	0	1.0258005	0.865	0.300	0
Cfl1	0	1.2196355	0.884	0.463	0
Man2b1	0	0.9932871	0.886	0.399	0
Cd52	0	0.6197818	0.738	0.187	0
Rps6	0	0.7430137	0.779	0.197	0
Rpl19	0	1.2497134	0.766	0.182	0
Cox4i1	0	1.3180256	0.795	0.227	0
Arfgef3	0	-4.0098038	0.574	0.833	0
Rps23-ps1	0	1.1017877	0.841	0.246	0
Rps16	0	0.9529365	0.817	0.246	0
Rplp2	0	0.7315401	0.793	0.207	0
AU020206	0	2.4513427	0.688	0.172	0
Rps28	0	1.0094138	0.891	0.291	0
Laptm5	0	1.2047213	0.969	0.665	0
Rpl3	0	1.4624131	0.773	0.232	0
Ppt1	0	1.4212335	0.749	0.246	0
Lamp1	0	0.4694796	0.915	0.448	0
Creg1	0	0.9666021	0.773	0.251	0
B2m	0	0.9439195	0.989	0.734	0
Hif1a	0	3.1804196	0.587	0.074	0
Rpl15	0	0.8104652	0.749	0.182	0
Rpl13	0	0.7091759	0.880	0.305	0
Rpl35a	0	0.5728594	0.736	0.172	0
Cd83	0	3.1097143	0.629	0.128	0
Rpl32	0	0.0061385	0.882	0.305	0
Rbm45	0	-5.0699120	0.594	0.828	0
Hsp90b1	0	0.6376631	0.841	0.330	0
Pdia3	0	1.0331859	0.828	0.325	0
Rps8	0	1.5908680	0.714	0.187	0
Ctss	0	0.9543452	1.000	0.847	0
Ccl3	0	4.4857741	0.533	0.044	0
Dnajb14	0	2.3303873	0.692	0.177	0
Cadm1	0	1.7429086	0.651	0.143	0
Gnas	0	1.7107747	0.734	0.212	0
Rpl10a	0	0.2706754	0.801	0.261	0
Psap	0	0.9238396	0.985	0.626	0
Rpl18	0	0.7048072	0.740	0.207	0

Microglia2_vs_Microglia4

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-52.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Ifit3	0	-6.2941243	0.061	0.628	0.00e+00
Rtp4	0	-2.8837830	0.201	0.717	0.00e+00
Iigp1	0	-5.1929461	0.107	0.558	0.00e+00
Mx1	0	-5.4224647	0.096	0.522	0.00e+00
Ifit3b	0	-6.8333059	0.096	0.504	0.00e+00
Ifit2	0	-5.0561604	0.055	0.425	0.00e+00
Stat1	0	-2.5846951	0.371	0.823	0.00e+00
Iigp1c	0	-4.3730970	0.175	0.602	0.00e+00
Usp18	0	-4.2910116	0.103	0.504	0.00e+00
Ifi206	0	-5.4664697	0.024	0.319	0.00e+00
Tgtp2	0	-4.2713872	0.052	0.389	0.00e+00
Oasl2	0	-3.4547280	0.264	0.673	0.00e+00
Ccl12	0	-2.8636234	0.269	0.690	0.00e+00
Irf7	0	-3.6899477	0.068	0.398	0.00e+00
Oas2	0	-4.3154382	0.037	0.327	0.00e+00
Ifi209	0	-3.3486548	0.111	0.469	0.00e+00
Lyz2	0	1.4579243	0.921	0.708	0.00e+00
Rnf213	0	-2.6668510	0.229	0.628	0.00e+00
Trim30a	0	-1.8304591	0.371	0.726	0.00e+00
Apoe	0	1.5814612	0.937	0.726	0.00e+00
Clec7a	0	2.2502925	0.668	0.204	0.00e+00
Ifit1	0	-4.7023280	0.079	0.363	0.00e+00
Cst7	0	2.2102465	0.705	0.310	0.00e+00
Rsad2	0	-6.7067931	0.057	0.319	0.00e+00
Ctsb	0	0.9625566	0.993	0.965	0.00e+00
Ifi211	0	-4.3361877	0.039	0.283	0.00e+00
Ifi204	0	-2.7640857	0.417	0.726	0.00e+00
Oas1g	0	-2.8546893	0.103	0.407	0.00e+00
Ifi213	0	-4.5743985	0.203	0.513	0.00e+00
Nlrc5	0	-2.9669339	0.118	0.425	0.00e+00
Herc6	0	-2.9517754	0.367	0.681	0.00e+00
Ftl1	0	0.9448623	0.976	0.938	0.00e+00
Trex1	0	-1.8325374	0.231	0.575	0.00e+00
Irgm2	0	-2.7177538	0.148	0.460	0.00e+00
Cd63	0	1.2527303	0.893	0.664	0.00e+00
Phf11a	0	-3.7830704	0.076	0.345	0.00e+00
Fcgr1	0	-1.3568162	0.596	0.850	0.00e+00
Helz2	0	-5.0585094	0.017	0.195	0.00e+00
Ifi208	0	-3.8124370	0.159	0.469	0.00e+00
Slfn8	0	-2.6128055	0.360	0.673	0.00e+00
Oas1a	0	-2.3506154	0.153	0.460	0.00e+00
Ifitm3	0	-2.2095517	0.271	0.566	0.00e+00
Isg15	0	-3.4470726	0.179	0.460	0.00e+00
Trim30d	0	-2.3151606	0.255	0.584	0.00e+00
Ctsd	0	0.8606491	1.000	0.991	0.00e+00
Parp14	0	-3.1715874	0.245	0.531	0.00e+00
Selplg	0	-0.8109430	0.924	0.956	0.00e+00
Cd68	0	1.0343615	0.932	0.796	0.00e+00
Ly6a	0	-3.6771203	0.024	0.204	0.00e+00
Mx2	0	-3.0539106	0.072	0.310	0.00e+00
Zbp1	0	-3.1645428	0.109	0.363	0.00e+00
Gapdh	0	1.2064431	0.841	0.664	0.00e+00
Ccl3	0	2.7723928	0.533	0.159	0.00e+00
Ms4a6b	0	-2.1935614	0.170	0.460	0.00e+00
Tyrobp	0	1.1163903	0.980	0.965	1.00e-07
Phf11b	0	-2.5719599	0.131	0.389	2.00e-07
Irgm1	0	-2.7120912	0.295	0.549	2.00e-07
Ifi214	0	-3.1527124	0.177	0.451	2.00e-07
Rsrp1	0	-0.9305697	0.854	0.956	2.00e-07
Serinc3	0	-0.6556931	0.976	1.000	3.00e-07
Dhx58	0	-2.3835526	0.138	0.398	3.00e-07
Xaf1	0	-1.8940135	0.469	0.708	3.00e-07
Tmem119	0	-1.0362580	0.760	0.912	4.00e-07
Slfn2	0	-2.5330386	0.212	0.487	4.00e-07
Ctsa	0	0.8417328	0.959	0.876	7.00e-07
Eef1a1	0	0.6999194	0.989	0.965	9.00e-07
Fgl2	0	-2.5704249	0.179	0.442	1.70e-06
Atp6v0a2	0	-1.2278861	0.260	0.575	2.10e-06
Phf11d	0	-2.7701409	0.190	0.442	3.00e-06
P2ry12	0	-0.8110582	0.915	0.965	3.50e-06
Igtp	0	-2.4375314	0.181	0.434	3.80e-06
Gbp7	0	-3.8054657	0.100	0.319	4.20e-06
Pmp22	0	1.4877775	0.694	0.425	4.40e-06
Samd9l	0	-2.9468343	0.061	0.257	4.60e-06
Rigi	0	-2.8987722	0.469	0.673	4.90e-06
Lpl	0	3.3037468	0.825	0.708	5.20e-06
Dapp1	0	-1.8386634	0.271	0.540	5.80e-06
Tor3a	0	-2.0779994	0.242	0.496	7.30e-06
Rpl35rt	0	0.9474910	0.915	0.779	7.60e-06
Sp100	0	-2.1235346	0.358	0.611	8.60e-06
Oasl1	0	-6.1754000	0.028	0.177	8.80e-06
Parp12	0	-2.1341265	0.166	0.416	1.08e-05
Hif1a	0	1.8217006	0.587	0.274	1.08e-05
Ifi207	0	-2.4107599	0.120	0.354	1.23e-05
Ifi205	0	-2.5142149	0.022	0.159	2.19e-05
Ctsz	0	0.6776589	0.987	0.947	2.21e-05
Mif	0	1.5134573	0.605	0.319	2.62e-05
Etnk1	0	-1.7001717	0.314	0.575	2.97e-05
Dtx3l	0	-1.5235479	0.426	0.690	3.45e-05
Ifi47	0	-7.4854128	0.004	0.097	4.22e-05
Morc3	0	-1.6687019	0.297	0.558	4.27e-05
Frmd4a	0	-0.9326993	0.627	0.858	4.37e-05
Cmpk2	0	-3.7385669	0.024	0.159	4.44e-05
Rpl21	0	1.0010398	0.856	0.619	5.91e-05
Slfn5	0	-2.7671553	0.517	0.717	5.99e-05
Fth1	0	0.6611646	0.983	0.920	6.90e-05
Ctsl	0	0.8069538	0.969	0.938	7.08e-05
Syngr1	0	1.2318438	0.810	0.611	7.43e-05
Gnas	0	1.2406783	0.734	0.451	7.80e-05
Ddx60	0	-2.5908945	0.153	0.381	8.87e-05

Microglia2_vs_Microglia4_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-55.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Ifit3	0	-6.2941243	0.061	0.628	0.00e+00
Rtp4	0	-2.8837830	0.201	0.717	0.00e+00
Iigp1	0	-5.1929461	0.107	0.558	0.00e+00
Mx1	0	-5.4224647	0.096	0.522	0.00e+00
Ifit3b	0	-6.8333059	0.096	0.504	0.00e+00
Ifit2	0	-5.0561604	0.055	0.425	0.00e+00
Stat1	0	-2.5846951	0.371	0.823	0.00e+00
Iigp1c	0	-4.3730970	0.175	0.602	0.00e+00
Usp18	0	-4.2910116	0.103	0.504	0.00e+00
Ifi206	0	-5.4664697	0.024	0.319	0.00e+00
Tgtp2	0	-4.2713872	0.052	0.389	0.00e+00
Oasl2	0	-3.4547280	0.264	0.673	0.00e+00
Ccl12	0	-2.8636234	0.269	0.690	0.00e+00
Irf7	0	-3.6899477	0.068	0.398	0.00e+00
Oas2	0	-4.3154382	0.037	0.327	0.00e+00
Ifi209	0	-3.3486548	0.111	0.469	0.00e+00
Lyz2	0	1.4579243	0.921	0.708	0.00e+00
Rnf213	0	-2.6668510	0.229	0.628	0.00e+00
Trim30a	0	-1.8304591	0.371	0.726	0.00e+00
Apoe	0	1.5814612	0.937	0.726	0.00e+00
Clec7a	0	2.2502925	0.668	0.204	0.00e+00
Ifit1	0	-4.7023280	0.079	0.363	0.00e+00
Cst7	0	2.2102465	0.705	0.310	0.00e+00
Rsad2	0	-6.7067931	0.057	0.319	0.00e+00
Ctsb	0	0.9625566	0.993	0.965	0.00e+00
Ifi211	0	-4.3361877	0.039	0.283	0.00e+00
Ifi204	0	-2.7640857	0.417	0.726	0.00e+00
Oas1g	0	-2.8546893	0.103	0.407	0.00e+00
Ifi213	0	-4.5743985	0.203	0.513	0.00e+00
Nlrc5	0	-2.9669339	0.118	0.425	0.00e+00
Herc6	0	-2.9517754	0.367	0.681	0.00e+00
Ftl1	0	0.9448623	0.976	0.938	0.00e+00
Trex1	0	-1.8325374	0.231	0.575	0.00e+00
Irgm2	0	-2.7177538	0.148	0.460	0.00e+00
Cd63	0	1.2527303	0.893	0.664	0.00e+00
Phf11a	0	-3.7830704	0.076	0.345	0.00e+00
Fcgr1	0	-1.3568162	0.596	0.850	0.00e+00
Helz2	0	-5.0585094	0.017	0.195	0.00e+00
Ifi208	0	-3.8124370	0.159	0.469	0.00e+00
Slfn8	0	-2.6128055	0.360	0.673	0.00e+00
Oas1a	0	-2.3506154	0.153	0.460	0.00e+00
Ifitm3	0	-2.2095517	0.271	0.566	0.00e+00
Isg15	0	-3.4470726	0.179	0.460	0.00e+00
Trim30d	0	-2.3151606	0.255	0.584	0.00e+00
Ctsd	0	0.8606491	1.000	0.991	0.00e+00
Parp14	0	-3.1715874	0.245	0.531	0.00e+00
Selplg	0	-0.8109430	0.924	0.956	0.00e+00
Cd68	0	1.0343615	0.932	0.796	0.00e+00
Ly6a	0	-3.6771203	0.024	0.204	0.00e+00
Mx2	0	-3.0539106	0.072	0.310	0.00e+00
Zbp1	0	-3.1645428	0.109	0.363	0.00e+00
Gapdh	0	1.2064431	0.841	0.664	0.00e+00
Ccl3	0	2.7723928	0.533	0.159	0.00e+00
Ms4a6b	0	-2.1935614	0.170	0.460	0.00e+00
Tyrobp	0	1.1163903	0.980	0.965	1.00e-07
Phf11b	0	-2.5719599	0.131	0.389	2.00e-07
Irgm1	0	-2.7120912	0.295	0.549	2.00e-07
Ifi214	0	-3.1527124	0.177	0.451	2.00e-07
Rsrp1	0	-0.9305697	0.854	0.956	2.00e-07
Serinc3	0	-0.6556931	0.976	1.000	3.00e-07
Dhx58	0	-2.3835526	0.138	0.398	3.00e-07
Xaf1	0	-1.8940135	0.469	0.708	3.00e-07
Tmem119	0	-1.0362580	0.760	0.912	4.00e-07
Slfn2	0	-2.5330386	0.212	0.487	4.00e-07
Ctsa	0	0.8417328	0.959	0.876	7.00e-07
Eef1a1	0	0.6999194	0.989	0.965	9.00e-07
Fgl2	0	-2.5704249	0.179	0.442	1.70e-06
Atp6v0a2	0	-1.2278861	0.260	0.575	2.10e-06
Phf11d	0	-2.7701409	0.190	0.442	3.00e-06
P2ry12	0	-0.8110582	0.915	0.965	3.50e-06
Igtp	0	-2.4375314	0.181	0.434	3.80e-06
Gbp7	0	-3.8054657	0.100	0.319	4.20e-06
Pmp22	0	1.4877775	0.694	0.425	4.40e-06
Samd9l	0	-2.9468343	0.061	0.257	4.60e-06
Rigi	0	-2.8987722	0.469	0.673	4.90e-06
Lpl	0	3.3037468	0.825	0.708	5.20e-06
Dapp1	0	-1.8386634	0.271	0.540	5.80e-06
Tor3a	0	-2.0779994	0.242	0.496	7.30e-06
Rpl35rt	0	0.9474910	0.915	0.779	7.60e-06
Sp100	0	-2.1235346	0.358	0.611	8.60e-06
Oasl1	0	-6.1754000	0.028	0.177	8.80e-06
Parp12	0	-2.1341265	0.166	0.416	1.08e-05
Hif1a	0	1.8217006	0.587	0.274	1.08e-05
Ifi207	0	-2.4107599	0.120	0.354	1.23e-05
Ifi205	0	-2.5142149	0.022	0.159	2.19e-05
Ctsz	0	0.6776589	0.987	0.947	2.21e-05
Mif	0	1.5134573	0.605	0.319	2.62e-05
Etnk1	0	-1.7001717	0.314	0.575	2.97e-05
Dtx3l	0	-1.5235479	0.426	0.690	3.45e-05
Ifi47	0	-7.4854128	0.004	0.097	4.22e-05
Morc3	0	-1.6687019	0.297	0.558	4.27e-05
Frmd4a	0	-0.9326993	0.627	0.858	4.37e-05
Cmpk2	0	-3.7385669	0.024	0.159	4.44e-05
Rpl21	0	1.0010398	0.856	0.619	5.91e-05
Slfn5	0	-2.7671553	0.517	0.717	5.99e-05
Fth1	0	0.6611646	0.983	0.920	6.90e-05
Ctsl	0	0.8069538	0.969	0.938	7.08e-05
Syngr1	0	1.2318438	0.810	0.611	7.43e-05
Gnas	0	1.2406783	0.734	0.451	7.80e-05
Ddx60	0	-2.5908945	0.153	0.381	8.87e-05

Microglia2_vs_Microglia5

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-58.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0000000	-5.3451229	0.144	0.904	0.0000000
H2-Eb1	0.0000000	-7.1667700	0.031	0.630	0.0000000
H2-Aa	0.0000000	-6.2384326	0.109	0.712	0.0000000
Cd74	0.0000000	-4.7767701	0.443	0.959	0.0000000
Apoe	0.0000000	2.4085403	0.937	0.753	0.0000000
Selplg	0.0000000	-1.0407621	0.924	0.986	0.0000002
Cd63	0.0000000	1.2786389	0.893	0.685	0.0000008
H2-D1	0.0000000	-0.9645578	0.941	0.959	0.0000048
Rpl35rt	0.0000000	1.2894276	0.915	0.685	0.0000089
Lyz2	0.0000000	1.0563367	0.921	0.685	0.0000115
P2ry12	0.0000000	-1.1235935	0.915	0.959	0.0000160
Tmem119	0.0000000	-1.2422070	0.760	0.877	0.0001208
Ftl1	0.0000000	0.7586969	0.976	0.973	0.0003264
Lpl	0.0000000	2.5225444	0.825	0.616	0.0007345
Hoxb1	0.0000001	-0.9117428	0.105	0.342	0.0011121
Fth1	0.0000001	0.7333233	0.983	1.000	0.0016283
Ctsz	0.0000001	0.6747200	0.987	0.890	0.0017341
Clec7a	0.0000001	1.1260543	0.668	0.288	0.0020302
Gnas	0.0000002	1.3946833	0.734	0.438	0.0027413
Cst7	0.0000002	1.0062695	0.705	0.301	0.0030008
Csf1r	0.0000002	-0.5243534	0.991	1.000	0.0036012
Irgm2	0.0000004	-2.0859889	0.148	0.384	0.0058809
Ccl3	0.0000005	2.9802710	0.533	0.260	0.0079733
Jcad	0.0000005	-4.8386824	0.000	0.055	0.0081954
Mt1	0.0000008	1.1930677	0.594	0.288	0.0124939
Ftl1-ps1	0.0000008	1.5767103	0.779	0.562	0.0129632
Hrh2	0.0000012	-4.7767855	0.033	0.164	0.0184060
Rpl21	0.0000013	0.9058642	0.856	0.630	0.0202140
Rpl7	0.0000019	1.0947626	0.930	0.822	0.0308589
Ccl4	0.0000023	3.1030600	0.332	0.055	0.0362273
Hif1a	0.0000027	1.4173114	0.587	0.274	0.0428335
Tpst2	0.0000030	-1.8131180	0.273	0.493	0.0477700
Ctsb	0.0000036	0.5891559	0.993	0.959	0.0573673
Pfkm	0.0000038	-2.5260504	0.007	0.082	0.0607689
Tpt1	0.0000053	0.8034978	0.825	0.589	0.0846516
Upk1b	0.0000066	-2.1526737	0.094	0.274	0.1044726
Rpl13a	0.0000068	0.6557451	0.917	0.808	0.1090125
Zfp109	0.0000086	-3.1435187	0.004	0.068	0.1364508
H2-K1	0.0000111	-0.7444660	0.900	0.932	0.1765875
Siglech	0.0000115	-0.8672070	0.882	0.945	0.1826192
Rpl35	0.0000148	0.9585920	0.928	0.753	0.2367280
Mmp28	0.0000166	-1.9845774	0.002	0.055	0.2648944
Tnc	0.0000166	-2.3775443	0.002	0.055	0.2648944
Cd68	0.0000178	0.6524691	0.932	0.877	0.2836960
Rplp1	0.0000188	0.6910374	0.932	0.822	0.2994568
Rps25	0.0000200	0.7754654	0.865	0.753	0.3189262
Ciita	0.0000216	-4.8095763	0.028	0.137	0.3442854
P2ry13	0.0000223	-0.9586586	0.701	0.849	0.3549733
Lilrb4a	0.0000230	2.6716423	0.345	0.110	0.3665061
Fgd2	0.0000268	-1.2655078	0.522	0.685	0.4278358
C3ar1	0.0000271	1.0458375	0.664	0.438	0.4314617
H2-Oa	0.0000290	-1.7206777	0.162	0.356	0.4616728
Rps9	0.0000296	0.6099635	0.884	0.753	0.4723822
Susd3	0.0000300	-1.2473605	0.500	0.658	0.4783200
Rps26	0.0000309	0.6608937	0.742	0.479	0.4921130
Ctsd	0.0000318	0.4789682	1.000	0.973	0.5078206
Eif4a1	0.0000320	1.0686170	0.769	0.562	0.5103260
Rpl41	0.0000346	0.6099427	0.930	0.795	0.5520143
Rpl18a	0.0000371	0.4685572	0.952	0.863	0.5912313
Gusb	0.0000423	1.0873203	0.793	0.644	0.6743211
Il17ra	0.0000443	-1.9969095	0.293	0.493	0.7059775
Cmtm7	0.0000472	-1.2546507	0.439	0.644	0.7530573
Apbb2	0.0000525	1.6106863	0.459	0.205	0.8374611
Rpl7a	0.0000636	0.7322386	0.699	0.466	1.0000000
Ndufb2	0.0000656	2.5001517	0.504	0.315	1.0000000
Rps28	0.0000672	0.7057895	0.891	0.808	1.0000000
Rnase6	0.0000707	-1.3677990	0.068	0.205	1.0000000
Rpl18	0.0000709	0.8570031	0.740	0.479	1.0000000
Cx3cr1	0.0000844	-0.5724904	0.972	0.945	1.0000000
Adamts6	0.0000859	-0.8170736	0.026	0.123	1.0000000
Prkca	0.0000873	-2.1854205	0.105	0.260	1.0000000
Mir8114	0.0000896	-1.8108627	0.186	0.384	1.0000000
Tpd52	0.0000897	1.0237119	0.633	0.397	1.0000000
Pld4	0.0000902	-0.7632094	0.803	0.904	1.0000000
Cmtm6	0.0000934	-1.1980312	0.592	0.767	1.0000000
Cd9	0.0000954	0.5419159	0.969	0.945	1.0000000
Smim29	0.0001133	1.7796118	0.334	0.110	1.0000000
Glul	0.0001292	-0.8817242	0.655	0.808	1.0000000
Rnase4	0.0001348	-0.5705109	0.797	0.932	1.0000000
Rpl37a	0.0001369	0.5922122	0.865	0.726	1.0000000
Uba52rt	0.0001420	0.7456597	0.755	0.589	1.0000000
Myo1e	0.0001421	1.7887827	0.358	0.137	1.0000000
Plaur	0.0001527	2.4814429	0.290	0.082	1.0000000
Ltb	0.0001541	-3.9409280	0.004	0.055	1.0000000
Uba52	0.0001550	0.6482223	0.812	0.589	1.0000000
Cd81	0.0001556	-0.3331951	0.991	1.000	1.0000000
Colec10	0.0001626	-3.5311507	0.004	0.055	1.0000000
Dcst1	0.0001668	-2.1432968	0.146	0.315	1.0000000
Or5v1b	0.0001706	0.4972863	0.247	0.041	1.0000000
Malat1	0.0001733	-0.2811189	0.952	0.973	1.0000000
H2-Q7	0.0001774	-2.1227370	0.454	0.603	1.0000000
Dnajc12	0.0001815	-0.7394357	0.308	0.534	1.0000000
Serf2	0.0001857	0.8133924	0.784	0.575	1.0000000
Rps12l1	0.0001875	1.4113647	0.629	0.425	1.0000000
Sesn1	0.0002018	-1.7074962	0.225	0.411	1.0000000
Axl	0.0002025	1.1336636	0.533	0.301	1.0000000
Slc13a3	0.0002125	-3.3341157	0.024	0.110	1.0000000
Rpl3	0.0002196	0.8025449	0.773	0.603	1.0000000
Rplp0	0.0002304	0.7392331	0.852	0.712	1.0000000
Cd63-ps	0.0002323	0.6916063	0.328	0.110	1.0000000

Microglia2_vs_Microglia5_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-61.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0000000	-5.3451229	0.144	0.904	0.0000000
H2-Eb1	0.0000000	-7.1667700	0.031	0.630	0.0000000
H2-Aa	0.0000000	-6.2384326	0.109	0.712	0.0000000
Cd74	0.0000000	-4.7767701	0.443	0.959	0.0000000
Apoe	0.0000000	2.4085403	0.937	0.753	0.0000000
Selplg	0.0000000	-1.0407621	0.924	0.986	0.0000002
Cd63	0.0000000	1.2786389	0.893	0.685	0.0000008
H2-D1	0.0000000	-0.9645578	0.941	0.959	0.0000048
Rpl35rt	0.0000000	1.2894276	0.915	0.685	0.0000089
Lyz2	0.0000000	1.0563367	0.921	0.685	0.0000115
P2ry12	0.0000000	-1.1235935	0.915	0.959	0.0000160
Tmem119	0.0000000	-1.2422070	0.760	0.877	0.0001208
Ftl1	0.0000000	0.7586969	0.976	0.973	0.0003264
Lpl	0.0000000	2.5225444	0.825	0.616	0.0007345
Hoxb1	0.0000001	-0.9117428	0.105	0.342	0.0011121
Fth1	0.0000001	0.7333233	0.983	1.000	0.0016283
Ctsz	0.0000001	0.6747200	0.987	0.890	0.0017341
Clec7a	0.0000001	1.1260543	0.668	0.288	0.0020302
Gnas	0.0000002	1.3946833	0.734	0.438	0.0027413
Cst7	0.0000002	1.0062695	0.705	0.301	0.0030008
Csf1r	0.0000002	-0.5243534	0.991	1.000	0.0036012
Irgm2	0.0000004	-2.0859889	0.148	0.384	0.0058809
Ccl3	0.0000005	2.9802710	0.533	0.260	0.0079733
Jcad	0.0000005	-4.8386824	0.000	0.055	0.0081954
Mt1	0.0000008	1.1930677	0.594	0.288	0.0124939
Ftl1-ps1	0.0000008	1.5767103	0.779	0.562	0.0129632
Hrh2	0.0000012	-4.7767855	0.033	0.164	0.0184060
Rpl21	0.0000013	0.9058642	0.856	0.630	0.0202140
Rpl7	0.0000019	1.0947626	0.930	0.822	0.0308589
Ccl4	0.0000023	3.1030600	0.332	0.055	0.0362273
Hif1a	0.0000027	1.4173114	0.587	0.274	0.0428335
Tpst2	0.0000030	-1.8131180	0.273	0.493	0.0477700
Ctsb	0.0000036	0.5891559	0.993	0.959	0.0573673
Pfkm	0.0000038	-2.5260504	0.007	0.082	0.0607689
Tpt1	0.0000053	0.8034978	0.825	0.589	0.0846516
Upk1b	0.0000066	-2.1526737	0.094	0.274	0.1044726
Rpl13a	0.0000068	0.6557451	0.917	0.808	0.1090125
Zfp109	0.0000086	-3.1435187	0.004	0.068	0.1364508
H2-K1	0.0000111	-0.7444660	0.900	0.932	0.1765875
Siglech	0.0000115	-0.8672070	0.882	0.945	0.1826192
Rpl35	0.0000148	0.9585920	0.928	0.753	0.2367280
Mmp28	0.0000166	-1.9845774	0.002	0.055	0.2648944
Tnc	0.0000166	-2.3775443	0.002	0.055	0.2648944
Cd68	0.0000178	0.6524691	0.932	0.877	0.2836960
Rplp1	0.0000188	0.6910374	0.932	0.822	0.2994568
Rps25	0.0000200	0.7754654	0.865	0.753	0.3189262
Ciita	0.0000216	-4.8095763	0.028	0.137	0.3442854
P2ry13	0.0000223	-0.9586586	0.701	0.849	0.3549733
Lilrb4a	0.0000230	2.6716423	0.345	0.110	0.3665061
Fgd2	0.0000268	-1.2655078	0.522	0.685	0.4278358
C3ar1	0.0000271	1.0458375	0.664	0.438	0.4314617
H2-Oa	0.0000290	-1.7206777	0.162	0.356	0.4616728
Rps9	0.0000296	0.6099635	0.884	0.753	0.4723822
Susd3	0.0000300	-1.2473605	0.500	0.658	0.4783200
Rps26	0.0000309	0.6608937	0.742	0.479	0.4921130
Ctsd	0.0000318	0.4789682	1.000	0.973	0.5078206
Eif4a1	0.0000320	1.0686170	0.769	0.562	0.5103260
Rpl41	0.0000346	0.6099427	0.930	0.795	0.5520143
Rpl18a	0.0000371	0.4685572	0.952	0.863	0.5912313
Gusb	0.0000423	1.0873203	0.793	0.644	0.6743211
Il17ra	0.0000443	-1.9969095	0.293	0.493	0.7059775
Cmtm7	0.0000472	-1.2546507	0.439	0.644	0.7530573
Apbb2	0.0000525	1.6106863	0.459	0.205	0.8374611
Rpl7a	0.0000636	0.7322386	0.699	0.466	1.0000000
Ndufb2	0.0000656	2.5001517	0.504	0.315	1.0000000
Rps28	0.0000672	0.7057895	0.891	0.808	1.0000000
Rnase6	0.0000707	-1.3677990	0.068	0.205	1.0000000
Rpl18	0.0000709	0.8570031	0.740	0.479	1.0000000
Cx3cr1	0.0000844	-0.5724904	0.972	0.945	1.0000000
Adamts6	0.0000859	-0.8170736	0.026	0.123	1.0000000
Prkca	0.0000873	-2.1854205	0.105	0.260	1.0000000
Mir8114	0.0000896	-1.8108627	0.186	0.384	1.0000000
Tpd52	0.0000897	1.0237119	0.633	0.397	1.0000000
Pld4	0.0000902	-0.7632094	0.803	0.904	1.0000000
Cmtm6	0.0000934	-1.1980312	0.592	0.767	1.0000000
Cd9	0.0000954	0.5419159	0.969	0.945	1.0000000
Smim29	0.0001133	1.7796118	0.334	0.110	1.0000000
Glul	0.0001292	-0.8817242	0.655	0.808	1.0000000
Rnase4	0.0001348	-0.5705109	0.797	0.932	1.0000000
Rpl37a	0.0001369	0.5922122	0.865	0.726	1.0000000
Uba52rt	0.0001420	0.7456597	0.755	0.589	1.0000000
Myo1e	0.0001421	1.7887827	0.358	0.137	1.0000000
Plaur	0.0001527	2.4814429	0.290	0.082	1.0000000
Ltb	0.0001541	-3.9409280	0.004	0.055	1.0000000
Uba52	0.0001550	0.6482223	0.812	0.589	1.0000000
Cd81	0.0001556	-0.3331951	0.991	1.000	1.0000000
Colec10	0.0001626	-3.5311507	0.004	0.055	1.0000000
Dcst1	0.0001668	-2.1432968	0.146	0.315	1.0000000
Or5v1b	0.0001706	0.4972863	0.247	0.041	1.0000000
Malat1	0.0001733	-0.2811189	0.952	0.973	1.0000000
H2-Q7	0.0001774	-2.1227370	0.454	0.603	1.0000000
Dnajc12	0.0001815	-0.7394357	0.308	0.534	1.0000000
Serf2	0.0001857	0.8133924	0.784	0.575	1.0000000
Rps12l1	0.0001875	1.4113647	0.629	0.425	1.0000000
Sesn1	0.0002018	-1.7074962	0.225	0.411	1.0000000
Axl	0.0002025	1.1336636	0.533	0.301	1.0000000
Slc13a3	0.0002125	-3.3341157	0.024	0.110	1.0000000
Rpl3	0.0002196	0.8025449	0.773	0.603	1.0000000
Rplp0	0.0002304	0.7392331	0.852	0.712	1.0000000
Cd63-ps	0.0002323	0.6916063	0.328	0.110	1.0000000

Microglia3_vs_Microglia4

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-64.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Stat1	0	-3.8715741	0.108	0.823	0
Ccl12	0	-5.8058951	0.034	0.690	0
Oasl2	0	-8.9701768	0.034	0.673	0
Rtp4	0	-4.4318702	0.059	0.717	0
Ifit3	0	-10.2130141	0.020	0.628	0
Lgals3bp	0	-3.7784573	0.158	0.814	0
Ifi204	0	-2.5040501	0.113	0.726	0
Fcgr1	0	-1.6497400	0.232	0.850	0
H2-D1	0	-2.4643210	0.355	0.903	0
Ifi27l2a	0	-3.9338241	0.020	0.540	0
Rnf213	0	-3.7592791	0.074	0.628	0
Trim30a	0	-0.3563569	0.128	0.726	0
Iigp1c	0	-3.7352198	0.079	0.602	0
Usp18	0	-5.8754808	0.020	0.504	0
Ifit3b	0	-6.8947569	0.025	0.504	0
Psmb8	0	-2.0280511	0.108	0.690	0
Rab3gap1	0	-1.7515800	0.207	0.823	0
Ly6e	0	-2.0375461	0.404	0.912	0
Ifitm3	0	-2.5258656	0.074	0.566	0
Trim30d	0	-3.0262847	0.074	0.584	0
Mx1	0	-6.4073074	0.054	0.522	0
Iigp1	0	-4.8726788	0.069	0.558	0
Trex1	0	-4.0118002	0.089	0.575	0
Dtx3l	0	-0.8063297	0.148	0.690	0
Bst2	0	-3.5302365	0.069	0.558	0
Znfx1	0	-4.4684102	0.054	0.522	0
Rigi	0	-5.6755913	0.177	0.673	0
Oas1a	0	-4.4667086	0.020	0.460	0
Ifi209	0	-5.4750466	0.030	0.469	0
Gvin1	0	-3.4926248	0.089	0.593	0
Slfn2	0	-3.2134389	0.034	0.487	0
H2-T23	0	-2.7101540	0.281	0.779	0
Gvin2	0	-2.6178202	0.094	0.593	0
Frmd4a	0	-0.7291505	0.286	0.858	0
Ifit2	0	-6.6922227	0.015	0.425	0
Gvin-ps7	0	-3.5887785	0.079	0.558	0
Ifi213	0	-4.2683077	0.064	0.513	0
H2-K1	0	-1.9933750	0.389	0.841	0
Ctsd	0	-1.4319144	0.793	0.991	0
Xaf1	0	-2.1698091	0.202	0.708	0
Sp110	0	-4.2252854	0.059	0.513	0
Tgtp2	0	-9.5850755	0.005	0.389	0
Fgl2	0	-4.6728295	0.025	0.442	0
Irgm1	0	-3.3847754	0.084	0.549	0
Slc38a6	0	-0.7939891	0.369	0.894	0
Ctsz	0	-1.3676100	0.552	0.947	0
Nlrc5	0	-5.0470359	0.020	0.425	0
Ppp2r5a	0	-1.2606889	0.182	0.743	0
AU020206	0	-2.2173204	0.172	0.690	0
Samhd1	0	-1.1072513	0.177	0.717	0
Psap	0	-1.2073459	0.626	0.973	0
Serpine2	0	-1.6291886	0.369	0.876	0
Ctsh	0	-0.1872340	0.379	0.885	0
Serf2	0	-0.9470411	0.182	0.752	0
Grn	0	-1.2197911	0.473	0.938	0
Irf7	0	-7.5365346	0.015	0.398	0
Scamp2	0	-0.8571562	0.296	0.796	0
Rsrp1	0	-1.0764042	0.468	0.956	0
Parp14	0	-5.8054336	0.099	0.531	0
Slfn8	0	-1.3030567	0.167	0.673	0
Ctsb	0	-1.1516067	0.586	0.965	0
Tmcc3	0	-1.4966226	0.118	0.628	0
Oas1g	0	-4.0795742	0.020	0.407	0
Hexa	0	-0.9593763	0.409	0.894	0
Hsp90b1	0	-0.4787846	0.330	0.858	0
C1qa	0	-1.2082081	0.675	1.000	0
Zfp488	0	-1.5944163	0.192	0.752	0
C1qc	0	-1.1968656	0.729	0.991	0
Hmmr	0	-1.7717395	0.094	0.558	0
Ncl	0	-1.4222573	0.236	0.752	0
Psme1	0	-2.0139909	0.099	0.540	0
Laptm5	0	-1.2177837	0.665	0.965	0
Ifi207	0	-8.7601559	0.005	0.354	0
Cd9	0	-1.4140766	0.537	0.938	0
Ifi208	0	-4.3919174	0.054	0.469	0
Isg15	0	-4.2016957	0.054	0.460	0
Sgk3	0	-1.5027511	0.138	0.646	0
Man2b1	0	-0.9043467	0.399	0.885	0
Dcbld2	0	0.1416245	0.227	0.761	0
Rpl18a	0	-0.6125305	0.389	0.947	0
Sema4d	0	-1.7259783	0.187	0.681	0
Csf3r	0	-1.7711726	0.330	0.814	0
Parp9	0	-4.0149973	0.020	0.389	0
Pikfyve	0	-0.5615008	0.296	0.858	0
Tmbim6	0	-1.4821522	0.365	0.841	0
Ncf2	0	-0.1795121	0.222	0.735	0
Pdia3	0	-1.0344954	0.325	0.823	0
Herc6	0	-1.4670957	0.207	0.681	0
Atf2	0	-1.2207374	0.113	0.558	0
Ifi214	0	-3.9696484	0.049	0.451	0
Stat2	0	-2.8637168	0.158	0.619	0
Slfn9	0	-2.6545765	0.167	0.681	0
Eif2ak2	0	-0.8729874	0.286	0.779	0
Unc93b1	0	-0.6736716	0.365	0.894	0
Lag3	0	-1.3185418	0.340	0.814	0
Tmem234	0	-2.0836862	0.212	0.717	0
Zbp1	0	-6.5769951	0.015	0.363	0
Acot4	0	0.4015670	0.158	0.611	0
Fcgr2b	0	-0.5420644	0.300	0.867	0
Sfi1	0	-1.9027834	0.291	0.779	0

Microglia3_vs_Microglia4_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-67.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Stat1	0	-3.8715741	0.108	0.823	0
Ccl12	0	-5.8058951	0.034	0.690	0
Oasl2	0	-8.9701768	0.034	0.673	0
Rtp4	0	-4.4318702	0.059	0.717	0
Ifit3	0	-10.2130141	0.020	0.628	0
Lgals3bp	0	-3.7784573	0.158	0.814	0
Ifi204	0	-2.5040501	0.113	0.726	0
Fcgr1	0	-1.6497400	0.232	0.850	0
H2-D1	0	-2.4643210	0.355	0.903	0
Ifi27l2a	0	-3.9338241	0.020	0.540	0
Rnf213	0	-3.7592791	0.074	0.628	0
Trim30a	0	-0.3563569	0.128	0.726	0
Iigp1c	0	-3.7352198	0.079	0.602	0
Usp18	0	-5.8754808	0.020	0.504	0
Ifit3b	0	-6.8947569	0.025	0.504	0
Psmb8	0	-2.0280511	0.108	0.690	0
Rab3gap1	0	-1.7515800	0.207	0.823	0
Ly6e	0	-2.0375461	0.404	0.912	0
Ifitm3	0	-2.5258656	0.074	0.566	0
Trim30d	0	-3.0262847	0.074	0.584	0
Mx1	0	-6.4073074	0.054	0.522	0
Iigp1	0	-4.8726788	0.069	0.558	0
Trex1	0	-4.0118002	0.089	0.575	0
Dtx3l	0	-0.8063297	0.148	0.690	0
Bst2	0	-3.5302365	0.069	0.558	0
Znfx1	0	-4.4684102	0.054	0.522	0
Rigi	0	-5.6755913	0.177	0.673	0
Oas1a	0	-4.4667086	0.020	0.460	0
Ifi209	0	-5.4750466	0.030	0.469	0
Gvin1	0	-3.4926248	0.089	0.593	0
Slfn2	0	-3.2134389	0.034	0.487	0
H2-T23	0	-2.7101540	0.281	0.779	0
Gvin2	0	-2.6178202	0.094	0.593	0
Frmd4a	0	-0.7291505	0.286	0.858	0
Ifit2	0	-6.6922227	0.015	0.425	0
Gvin-ps7	0	-3.5887785	0.079	0.558	0
Ifi213	0	-4.2683077	0.064	0.513	0
H2-K1	0	-1.9933750	0.389	0.841	0
Ctsd	0	-1.4319144	0.793	0.991	0
Xaf1	0	-2.1698091	0.202	0.708	0
Sp110	0	-4.2252854	0.059	0.513	0
Tgtp2	0	-9.5850755	0.005	0.389	0
Fgl2	0	-4.6728295	0.025	0.442	0
Irgm1	0	-3.3847754	0.084	0.549	0
Slc38a6	0	-0.7939891	0.369	0.894	0
Ctsz	0	-1.3676100	0.552	0.947	0
Nlrc5	0	-5.0470359	0.020	0.425	0
Ppp2r5a	0	-1.2606889	0.182	0.743	0
AU020206	0	-2.2173204	0.172	0.690	0
Samhd1	0	-1.1072513	0.177	0.717	0
Psap	0	-1.2073459	0.626	0.973	0
Serpine2	0	-1.6291886	0.369	0.876	0
Ctsh	0	-0.1872340	0.379	0.885	0
Serf2	0	-0.9470411	0.182	0.752	0
Grn	0	-1.2197911	0.473	0.938	0
Irf7	0	-7.5365346	0.015	0.398	0
Scamp2	0	-0.8571562	0.296	0.796	0
Rsrp1	0	-1.0764042	0.468	0.956	0
Parp14	0	-5.8054336	0.099	0.531	0
Slfn8	0	-1.3030567	0.167	0.673	0
Ctsb	0	-1.1516067	0.586	0.965	0
Tmcc3	0	-1.4966226	0.118	0.628	0
Oas1g	0	-4.0795742	0.020	0.407	0
Hexa	0	-0.9593763	0.409	0.894	0
Hsp90b1	0	-0.4787846	0.330	0.858	0
C1qa	0	-1.2082081	0.675	1.000	0
Zfp488	0	-1.5944163	0.192	0.752	0
C1qc	0	-1.1968656	0.729	0.991	0
Hmmr	0	-1.7717395	0.094	0.558	0
Ncl	0	-1.4222573	0.236	0.752	0
Psme1	0	-2.0139909	0.099	0.540	0
Laptm5	0	-1.2177837	0.665	0.965	0
Ifi207	0	-8.7601559	0.005	0.354	0
Cd9	0	-1.4140766	0.537	0.938	0
Ifi208	0	-4.3919174	0.054	0.469	0
Isg15	0	-4.2016957	0.054	0.460	0
Sgk3	0	-1.5027511	0.138	0.646	0
Man2b1	0	-0.9043467	0.399	0.885	0
Dcbld2	0	0.1416245	0.227	0.761	0
Rpl18a	0	-0.6125305	0.389	0.947	0
Sema4d	0	-1.7259783	0.187	0.681	0
Csf3r	0	-1.7711726	0.330	0.814	0
Parp9	0	-4.0149973	0.020	0.389	0
Pikfyve	0	-0.5615008	0.296	0.858	0
Tmbim6	0	-1.4821522	0.365	0.841	0
Ncf2	0	-0.1795121	0.222	0.735	0
Pdia3	0	-1.0344954	0.325	0.823	0
Herc6	0	-1.4670957	0.207	0.681	0
Atf2	0	-1.2207374	0.113	0.558	0
Ifi214	0	-3.9696484	0.049	0.451	0
Stat2	0	-2.8637168	0.158	0.619	0
Slfn9	0	-2.6545765	0.167	0.681	0
Eif2ak2	0	-0.8729874	0.286	0.779	0
Unc93b1	0	-0.6736716	0.365	0.894	0
Lag3	0	-1.3185418	0.340	0.814	0
Tmem234	0	-2.0836862	0.212	0.717	0
Zbp1	0	-6.5769951	0.015	0.363	0
Acot4	0	0.4015670	0.158	0.611	0
Fcgr2b	0	-0.5420644	0.300	0.867	0
Sfi1	0	-1.9027834	0.291	0.779	0

Microglia3_vs_Microglia5

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-70.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Cd74	0	-9.3853200	0.039	0.959	0
H2-Ab1	0	-11.8268781	0.015	0.904	0
H2-Aa	0	-9.3473696	0.039	0.712	0
H2-Eb1	0	-10.4594799	0.010	0.630	0
H2-D1	0	-3.4064078	0.355	0.959	0
H2-K1	0	-2.4994716	0.389	0.932	0
Serpine2	0	-2.1643977	0.369	0.904	0
H2-T23	0	-2.7260109	0.281	0.808	0
Ctsd	0	-1.8135953	0.793	0.973	0
Laptm5	0	-1.5295736	0.665	0.986	0
Mef2c	0	-1.2526086	0.310	0.904	0
Rab3gap1	0	-1.4954167	0.207	0.781	0
Eif2a	0	4.5455464	0.941	0.808	0
Psap	0	-1.3221645	0.626	0.986	0
Rps2	0	-2.2932708	0.128	0.630	0
C1qa	0	-1.3886649	0.675	1.000	0
Syngr1	0	-2.3381513	0.256	0.753	0
Vmn1r13	0	5.3286250	0.946	0.726	0
Csf3r	0	-2.0938980	0.330	0.849	0
Ly86	0	-1.0619285	0.512	0.986	0
AU020206	0	-2.5151180	0.172	0.671	0
Ctsb	0	-1.5250075	0.586	0.959	0
Tmbim6	0	-1.6714603	0.365	0.877	0
Cd9	0	-1.5060192	0.537	0.945	0
C1qc	0	-1.3153308	0.729	1.000	0
Man2b1	0	-1.1501960	0.399	0.890	0
Trem2	0	-1.3833079	0.527	0.973	0
Or8b44	0	7.1029906	0.921	0.726	0
Ly6e	0	-1.9107258	0.404	0.863	0
Dnajb14	0	-1.7303235	0.177	0.685	0
Fth1	0	-0.9345402	0.581	1.000	0
Tyrobp	0	-1.7597110	0.562	0.973	0
Lrp1	0	-1.5176647	0.271	0.795	0
Hnrnpc	0	-2.3097710	0.172	0.685	0
H2-Oa	0	-4.9356767	0.020	0.356	0
Mpeg1	0	-1.1099886	0.404	0.918	0
Ppp2r5a	0	-1.7063703	0.182	0.685	0
Arhgef40	0	-0.6717269	0.251	0.781	0
Inpp5d	0	-0.6580027	0.355	0.877	0
Hexa	0	-1.2092582	0.409	0.877	0
Tbxas1	0	-1.1538932	0.192	0.699	0
Ctsa	0	-0.8830622	0.502	0.945	0
Man2b2	0	-3.6810408	0.034	0.384	0
Stx7	0	-0.7127254	0.212	0.712	0
Ctsh	0	-0.2188387	0.379	0.836	0
St14	0	0.3535673	0.177	0.685	0
Pafah1b1	0	-1.6140958	0.064	0.452	0
Elob	0	-0.7162583	0.113	0.562	0
Gsk3b	0	-0.7844757	0.207	0.726	0
Uspl1	0	-2.3443760	0.044	0.411	0
Sh3bgrl3	0	-0.8573382	0.167	0.658	0
Psmb8	0	-1.2594989	0.108	0.562	0
Rnase4	0	-1.0772526	0.488	0.932	0
Ccni	0	-0.3496484	0.099	0.548	0
Rabgap1l	0	-2.0658830	0.163	0.630	0
Alg5	0	-1.9154445	0.089	0.507	0
Lipe	0	4.1779459	0.975	0.836	0
H2-Q7	0	-2.7364203	0.172	0.603	0
Grn	0	-1.1976512	0.473	0.890	0
Tmed10	0	-1.2438598	0.192	0.671	0
Cdk9	0	-1.0995925	0.064	0.438	0
Trac	0	5.3777173	0.823	0.644	0
Bin1	0	-0.4103864	0.227	0.740	0
Ctss	0	-0.9825570	0.847	1.000	0
Cd68	0	-0.5978695	0.399	0.877	0
Glmp	0	-1.4176084	0.197	0.658	0
Unc93b1	0	-0.8150072	0.365	0.863	0
Ubl5	0	-0.0670143	0.153	0.603	0
Ftl1	0	-0.9576266	0.517	0.973	0
Gng5	0	-1.2399232	0.099	0.534	0
C1qb	0	-1.1289828	0.749	0.986	0
Csf1r	0	-1.0827861	0.759	1.000	0
Fyb1	0	-1.1133807	0.241	0.740	0
H2-Q10	0	-1.7575812	0.172	0.630	0
Dnajc12	0	-1.8431548	0.108	0.534	0
Atp6v0c	0	-1.5373524	0.296	0.740	0
Rnaset2a	0	-1.0878674	0.325	0.836	0
Rps16-ps2	0	-1.4871292	0.128	0.575	0
Cd300c2	0	-0.5001927	0.217	0.699	0
H2-DMa	0	-1.4773021	0.167	0.589	0
H2-M3	0	-1.9527795	0.054	0.411	0
Efhd2	0	-1.1526676	0.158	0.575	0
Slc46a3	0	-2.1091092	0.059	0.411	0
Arfgef3	0	3.9909418	0.833	0.658	0
Fcgr1	0	-1.1192498	0.232	0.685	0
mt-Nd4l	0	-0.9938295	0.222	0.685	0
Axl	0	-7.7884321	0.020	0.301	0
Rac1	0	-0.7403408	0.266	0.767	0
Cux2	0	4.1262726	0.906	0.795	0
Cep290	0	3.9076848	0.926	0.712	0
Sdf4	0	-2.0023669	0.143	0.548	0
Ypel3	0	-1.9443241	0.108	0.507	0
Rhoa	0	-0.6505675	0.315	0.808	0
Mlph	0	-2.7315945	0.133	0.575	0
Usp12	0	-3.7514392	0.074	0.425	0
Ywhah	0	-0.5799454	0.389	0.863	0
H2-Q6	0	-2.5397005	0.103	0.493	0
Ctsz	0	-1.3705490	0.552	0.890	0
Pld1	0	-1.9528670	0.256	0.712	0
Fcgr2b	0	-0.9513862	0.300	0.781	0

Microglia3_vs_Microglia5_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-73.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
Cd74	0	-9.3853200	0.039	0.959	0
H2-Ab1	0	-11.8268781	0.015	0.904	0
H2-Aa	0	-9.3473696	0.039	0.712	0
H2-Eb1	0	-10.4594799	0.010	0.630	0
H2-D1	0	-3.4064078	0.355	0.959	0
H2-K1	0	-2.4994716	0.389	0.932	0
Serpine2	0	-2.1643977	0.369	0.904	0
H2-T23	0	-2.7260109	0.281	0.808	0
Ctsd	0	-1.8135953	0.793	0.973	0
Laptm5	0	-1.5295736	0.665	0.986	0
Mef2c	0	-1.2526086	0.310	0.904	0
Rab3gap1	0	-1.4954167	0.207	0.781	0
Eif2a	0	4.5455464	0.941	0.808	0
Psap	0	-1.3221645	0.626	0.986	0
Rps2	0	-2.2932708	0.128	0.630	0
C1qa	0	-1.3886649	0.675	1.000	0
Syngr1	0	-2.3381513	0.256	0.753	0
Vmn1r13	0	5.3286250	0.946	0.726	0
Csf3r	0	-2.0938980	0.330	0.849	0
Ly86	0	-1.0619285	0.512	0.986	0
AU020206	0	-2.5151180	0.172	0.671	0
Ctsb	0	-1.5250075	0.586	0.959	0
Tmbim6	0	-1.6714603	0.365	0.877	0
Cd9	0	-1.5060192	0.537	0.945	0
C1qc	0	-1.3153308	0.729	1.000	0
Man2b1	0	-1.1501960	0.399	0.890	0
Trem2	0	-1.3833079	0.527	0.973	0
Or8b44	0	7.1029906	0.921	0.726	0
Ly6e	0	-1.9107258	0.404	0.863	0
Dnajb14	0	-1.7303235	0.177	0.685	0
Fth1	0	-0.9345402	0.581	1.000	0
Tyrobp	0	-1.7597110	0.562	0.973	0
Lrp1	0	-1.5176647	0.271	0.795	0
Hnrnpc	0	-2.3097710	0.172	0.685	0
H2-Oa	0	-4.9356767	0.020	0.356	0
Mpeg1	0	-1.1099886	0.404	0.918	0
Ppp2r5a	0	-1.7063703	0.182	0.685	0
Arhgef40	0	-0.6717269	0.251	0.781	0
Inpp5d	0	-0.6580027	0.355	0.877	0
Hexa	0	-1.2092582	0.409	0.877	0
Tbxas1	0	-1.1538932	0.192	0.699	0
Ctsa	0	-0.8830622	0.502	0.945	0
Man2b2	0	-3.6810408	0.034	0.384	0
Stx7	0	-0.7127254	0.212	0.712	0
Ctsh	0	-0.2188387	0.379	0.836	0
St14	0	0.3535673	0.177	0.685	0
Pafah1b1	0	-1.6140958	0.064	0.452	0
Elob	0	-0.7162583	0.113	0.562	0
Gsk3b	0	-0.7844757	0.207	0.726	0
Uspl1	0	-2.3443760	0.044	0.411	0
Sh3bgrl3	0	-0.8573382	0.167	0.658	0
Psmb8	0	-1.2594989	0.108	0.562	0
Rnase4	0	-1.0772526	0.488	0.932	0
Ccni	0	-0.3496484	0.099	0.548	0
Rabgap1l	0	-2.0658830	0.163	0.630	0
Alg5	0	-1.9154445	0.089	0.507	0
Lipe	0	4.1779459	0.975	0.836	0
H2-Q7	0	-2.7364203	0.172	0.603	0
Grn	0	-1.1976512	0.473	0.890	0
Tmed10	0	-1.2438598	0.192	0.671	0
Cdk9	0	-1.0995925	0.064	0.438	0
Trac	0	5.3777173	0.823	0.644	0
Bin1	0	-0.4103864	0.227	0.740	0
Ctss	0	-0.9825570	0.847	1.000	0
Cd68	0	-0.5978695	0.399	0.877	0
Glmp	0	-1.4176084	0.197	0.658	0
Unc93b1	0	-0.8150072	0.365	0.863	0
Ubl5	0	-0.0670143	0.153	0.603	0
Ftl1	0	-0.9576266	0.517	0.973	0
Gng5	0	-1.2399232	0.099	0.534	0
C1qb	0	-1.1289828	0.749	0.986	0
Csf1r	0	-1.0827861	0.759	1.000	0
Fyb1	0	-1.1133807	0.241	0.740	0
H2-Q10	0	-1.7575812	0.172	0.630	0
Dnajc12	0	-1.8431548	0.108	0.534	0
Atp6v0c	0	-1.5373524	0.296	0.740	0
Rnaset2a	0	-1.0878674	0.325	0.836	0
Rps16-ps2	0	-1.4871292	0.128	0.575	0
Cd300c2	0	-0.5001927	0.217	0.699	0
H2-DMa	0	-1.4773021	0.167	0.589	0
H2-M3	0	-1.9527795	0.054	0.411	0
Efhd2	0	-1.1526676	0.158	0.575	0
Slc46a3	0	-2.1091092	0.059	0.411	0
Arfgef3	0	3.9909418	0.833	0.658	0
Fcgr1	0	-1.1192498	0.232	0.685	0
mt-Nd4l	0	-0.9938295	0.222	0.685	0
Axl	0	-7.7884321	0.020	0.301	0
Rac1	0	-0.7403408	0.266	0.767	0
Cux2	0	4.1262726	0.906	0.795	0
Cep290	0	3.9076848	0.926	0.712	0
Sdf4	0	-2.0023669	0.143	0.548	0
Ypel3	0	-1.9443241	0.108	0.507	0
Rhoa	0	-0.6505675	0.315	0.808	0
Mlph	0	-2.7315945	0.133	0.575	0
Usp12	0	-3.7514392	0.074	0.425	0
Ywhah	0	-0.5799454	0.389	0.863	0
H2-Q6	0	-2.5397005	0.103	0.493	0
Ctsz	0	-1.3705490	0.552	0.890	0
Pld1	0	-1.9528670	0.256	0.712	0
Fcgr2b	0	-0.9513862	0.300	0.781	0

Microglia4_vs_Microglia5

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-76.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0000000	-6.7180526	0.035	0.904	0.0000000
Cd74	0.0000000	-4.8209626	0.257	0.959	0.0000000
H2-Aa	0.0000000	-6.0375032	0.106	0.712	0.0000000
H2-Eb1	0.0000000	-6.1621051	0.027	0.630	0.0000000
Ifit3	0.0000000	7.0195252	0.628	0.068	0.0000000
Rtp4	0.0000000	2.8367076	0.717	0.110	0.0000000
Ccl12	0.0000000	4.2299540	0.690	0.219	0.0000002
Trim30a	0.0000000	2.7661848	0.726	0.315	0.0000012
Oasl2	0.0000000	3.5298771	0.673	0.247	0.0000017
Mx1	0.0000000	6.1274782	0.522	0.123	0.0000217
Iigp1	0.0000000	5.0499900	0.558	0.123	0.0000218
Ifit3b	0.0000000	6.7744205	0.504	0.110	0.0000589
Stat1	0.0000000	1.8550486	0.823	0.466	0.0001113
Ifi204	0.0000000	2.3550192	0.726	0.342	0.0001307
Iigp1c	0.0000000	3.8414881	0.602	0.247	0.0001452
Ifitm3	0.0000000	2.9768778	0.566	0.178	0.0002150
Ifi213	0.0000000	3.5047205	0.513	0.137	0.0004443
Herc6	0.0000001	3.0351022	0.681	0.329	0.0012795
Ifi207	0.0000002	6.5949625	0.354	0.027	0.0028926
H2-D1	0.0000002	-0.9420868	0.903	0.959	0.0034501
Ifit2	0.0000003	4.0745665	0.425	0.082	0.0042823
Ifit1	0.0000003	6.7083986	0.363	0.041	0.0042910
Rnf213	0.0000003	1.8843658	0.628	0.219	0.0055075
Slfn5	0.0000003	3.7764428	0.717	0.411	0.0055480
Ifi206	0.0000005	5.8695650	0.319	0.014	0.0076853
Irf7	0.0000006	3.4349045	0.398	0.068	0.0091566
Oas1a	0.0000006	2.7870148	0.460	0.110	0.0092512
Usp18	0.0000007	3.5866099	0.504	0.178	0.0104704
Ifi214	0.0000014	3.4416636	0.451	0.123	0.0216193
Ifi209	0.0000021	3.3992342	0.469	0.164	0.0339346
Xaf1	0.0000029	2.5088532	0.708	0.479	0.0461421
Trex1	0.0000033	1.7773015	0.575	0.247	0.0529762
Oas2	0.0000046	3.7831455	0.327	0.041	0.0727644
Ifi208	0.0000048	3.2651998	0.469	0.137	0.0758662
Phf11a	0.0000063	3.4932374	0.345	0.055	0.1003983
Tgtp2	0.0000064	2.8919153	0.389	0.096	0.1013408
Ifi211	0.0000092	5.1271647	0.283	0.027	0.1474082
Atp6v0a2	0.0000141	0.8873805	0.575	0.219	0.2245107
Phf11b	0.0000186	2.1541175	0.389	0.110	0.2966558
Trim30d	0.0000190	1.7855877	0.584	0.301	0.3036422
Sp100	0.0000281	2.9139929	0.611	0.384	0.4482600
Nlrc5	0.0000296	2.4676577	0.425	0.137	0.4716227
Slfn8	0.0000348	2.1642037	0.673	0.438	0.5542296
Hmmr	0.0000359	1.8791510	0.558	0.260	0.5717086
Mx2	0.0000393	2.4805586	0.310	0.055	0.6265144
Rigi	0.0000457	3.7083975	0.673	0.521	0.7294898
Gvin2	0.0000544	1.9577801	0.593	0.288	0.8675028
Oas1g	0.0000562	0.8679367	0.407	0.123	0.8958727
Rsad2	0.0000608	5.9794145	0.319	0.082	0.9692005
Zc3hav1	0.0000620	2.3535287	0.549	0.315	0.9885789
Helz2	0.0000658	6.4845820	0.195	0.000	1.0000000
Isg20	0.0000658	5.4635086	0.195	0.000	1.0000000
Znfx1	0.0000670	1.9058425	0.522	0.233	1.0000000
Slfn2	0.0000677	3.4773890	0.487	0.260	1.0000000
Ms4a6b	0.0000708	2.5057945	0.460	0.205	1.0000000
Ifi27l2a	0.0000719	1.7247806	0.540	0.288	1.0000000
Zbp1	0.0000729	2.6578431	0.363	0.110	1.0000000
Irgm1	0.0000840	1.8493220	0.549	0.301	1.0000000
Uba7	0.0000842	1.6283294	0.487	0.205	1.0000000
Isg15	0.0001044	2.5363107	0.460	0.219	1.0000000
Bst2	0.0001222	1.2376012	0.558	0.274	1.0000000
Gvin1	0.0001611	1.8656888	0.593	0.288	1.0000000
Pml	0.0001896	4.3797669	0.336	0.110	1.0000000
Trafd1	0.0002011	1.5602221	0.496	0.233	1.0000000
Nmi	0.0002139	2.1638684	0.292	0.068	1.0000000
Tor3a	0.0002248	1.7232841	0.496	0.247	1.0000000
Lgals3bp	0.0002429	0.8641333	0.814	0.548	1.0000000
Gbp9	0.0002674	3.3944098	0.283	0.068	1.0000000
Phf11d	0.0002699	1.8343718	0.442	0.192	1.0000000
Parp9	0.0002977	3.1895987	0.389	0.164	1.0000000
BC005537	0.0003186	1.5327808	0.566	0.329	1.0000000
Parp14	0.0003618	1.7364523	0.531	0.288	1.0000000
Etnk1	0.0003639	1.0706114	0.575	0.315	1.0000000
Cacna2d3	0.0003645	2.8377693	0.212	0.027	1.0000000
Bglap3	0.0004380	1.7114147	0.186	0.014	1.0000000
Gvin-ps7	0.0004522	2.0859611	0.558	0.342	1.0000000
Slc25a23	0.0004737	1.6030931	0.301	0.082	1.0000000
Eif2ak2	0.0004816	1.3339524	0.779	0.616	1.0000000
Pim1	0.0005341	1.0745068	0.310	0.096	1.0000000
Fcgr1	0.0005507	0.5304902	0.850	0.685	1.0000000
Syngr1	0.0005960	-0.8745693	0.611	0.753	1.0000000
Oasl1	0.0006350	3.6416291	0.177	0.014	1.0000000
Yeats2	0.0006850	1.0615890	0.434	0.164	1.0000000
Usp12	0.0007114	-1.7635080	0.212	0.425	1.0000000
Or4m1	0.0007203	0.8873351	0.558	0.288	1.0000000
Ddx60	0.0007856	3.2313260	0.381	0.178	1.0000000
Rpl27rt	0.0007948	1.1872376	0.407	0.164	1.0000000
Dhx58	0.0008764	2.2083221	0.398	0.192	1.0000000
Tbc1d17	0.0008837	-1.9752687	0.212	0.438	1.0000000
Rdh14	0.0009081	2.5239321	0.221	0.041	1.0000000
Hspa4	0.0009162	1.5970181	0.319	0.110	1.0000000
Sass6	0.0009514	3.0759238	0.779	0.616	1.0000000
Mmp12	0.0009588	1.2198362	0.575	0.315	1.0000000
Smg9	0.0009894	2.7966054	0.451	0.233	1.0000000
Zfp12	0.0011424	4.3757188	0.274	0.082	1.0000000
Cmtm8	0.0011483	-3.4758316	0.088	0.260	1.0000000
Mtmr12	0.0012256	0.0965453	0.124	0.329	1.0000000
Ndufb2	0.0012750	2.6197800	0.513	0.315	1.0000000
Cnga3	0.0012920	1.4220726	0.319	0.110	1.0000000
Prkcd	0.0013160	0.6385280	0.717	0.493	1.0000000

Microglia4_vs_Microglia5_comorbid

\(`1` <img src="figure/scRNA_Analyses_Candlishetal.Rmd/unnamed-chunk-103-79.png" width="960" style="display: block; margin: auto;" />\)2 attr(,“class”) [1] “list” “ggarrange”

Markers

	p_val	avg_log2FC	pct.1	pct.2	p_val_adj
H2-Ab1	0.0000000	-6.7180526	0.035	0.904	0.0000000
Cd74	0.0000000	-4.8209626	0.257	0.959	0.0000000
H2-Aa	0.0000000	-6.0375032	0.106	0.712	0.0000000
H2-Eb1	0.0000000	-6.1621051	0.027	0.630	0.0000000
Ifit3	0.0000000	7.0195252	0.628	0.068	0.0000000
Rtp4	0.0000000	2.8367076	0.717	0.110	0.0000000
Ccl12	0.0000000	4.2299540	0.690	0.219	0.0000002
Trim30a	0.0000000	2.7661848	0.726	0.315	0.0000012
Oasl2	0.0000000	3.5298771	0.673	0.247	0.0000017
Mx1	0.0000000	6.1274782	0.522	0.123	0.0000217
Iigp1	0.0000000	5.0499900	0.558	0.123	0.0000218
Ifit3b	0.0000000	6.7744205	0.504	0.110	0.0000589
Stat1	0.0000000	1.8550486	0.823	0.466	0.0001113
Ifi204	0.0000000	2.3550192	0.726	0.342	0.0001307
Iigp1c	0.0000000	3.8414881	0.602	0.247	0.0001452
Ifitm3	0.0000000	2.9768778	0.566	0.178	0.0002150
Ifi213	0.0000000	3.5047205	0.513	0.137	0.0004443
Herc6	0.0000001	3.0351022	0.681	0.329	0.0012795
Ifi207	0.0000002	6.5949625	0.354	0.027	0.0028926
H2-D1	0.0000002	-0.9420868	0.903	0.959	0.0034501
Ifit2	0.0000003	4.0745665	0.425	0.082	0.0042823
Ifit1	0.0000003	6.7083986	0.363	0.041	0.0042910
Rnf213	0.0000003	1.8843658	0.628	0.219	0.0055075
Slfn5	0.0000003	3.7764428	0.717	0.411	0.0055480
Ifi206	0.0000005	5.8695650	0.319	0.014	0.0076853
Irf7	0.0000006	3.4349045	0.398	0.068	0.0091566
Oas1a	0.0000006	2.7870148	0.460	0.110	0.0092512
Usp18	0.0000007	3.5866099	0.504	0.178	0.0104704
Ifi214	0.0000014	3.4416636	0.451	0.123	0.0216193
Ifi209	0.0000021	3.3992342	0.469	0.164	0.0339346
Xaf1	0.0000029	2.5088532	0.708	0.479	0.0461421
Trex1	0.0000033	1.7773015	0.575	0.247	0.0529762
Oas2	0.0000046	3.7831455	0.327	0.041	0.0727644
Ifi208	0.0000048	3.2651998	0.469	0.137	0.0758662
Phf11a	0.0000063	3.4932374	0.345	0.055	0.1003983
Tgtp2	0.0000064	2.8919153	0.389	0.096	0.1013408
Ifi211	0.0000092	5.1271647	0.283	0.027	0.1474082
Atp6v0a2	0.0000141	0.8873805	0.575	0.219	0.2245107
Phf11b	0.0000186	2.1541175	0.389	0.110	0.2966558
Trim30d	0.0000190	1.7855877	0.584	0.301	0.3036422
Sp100	0.0000281	2.9139929	0.611	0.384	0.4482600
Nlrc5	0.0000296	2.4676577	0.425	0.137	0.4716227
Slfn8	0.0000348	2.1642037	0.673	0.438	0.5542296
Hmmr	0.0000359	1.8791510	0.558	0.260	0.5717086
Mx2	0.0000393	2.4805586	0.310	0.055	0.6265144
Rigi	0.0000457	3.7083975	0.673	0.521	0.7294898
Gvin2	0.0000544	1.9577801	0.593	0.288	0.8675028
Oas1g	0.0000562	0.8679367	0.407	0.123	0.8958727
Rsad2	0.0000608	5.9794145	0.319	0.082	0.9692005
Zc3hav1	0.0000620	2.3535287	0.549	0.315	0.9885789
Helz2	0.0000658	6.4845820	0.195	0.000	1.0000000
Isg20	0.0000658	5.4635086	0.195	0.000	1.0000000
Znfx1	0.0000670	1.9058425	0.522	0.233	1.0000000
Slfn2	0.0000677	3.4773890	0.487	0.260	1.0000000
Ms4a6b	0.0000708	2.5057945	0.460	0.205	1.0000000
Ifi27l2a	0.0000719	1.7247806	0.540	0.288	1.0000000
Zbp1	0.0000729	2.6578431	0.363	0.110	1.0000000
Irgm1	0.0000840	1.8493220	0.549	0.301	1.0000000
Uba7	0.0000842	1.6283294	0.487	0.205	1.0000000
Isg15	0.0001044	2.5363107	0.460	0.219	1.0000000
Bst2	0.0001222	1.2376012	0.558	0.274	1.0000000
Gvin1	0.0001611	1.8656888	0.593	0.288	1.0000000
Pml	0.0001896	4.3797669	0.336	0.110	1.0000000
Trafd1	0.0002011	1.5602221	0.496	0.233	1.0000000
Nmi	0.0002139	2.1638684	0.292	0.068	1.0000000
Tor3a	0.0002248	1.7232841	0.496	0.247	1.0000000
Lgals3bp	0.0002429	0.8641333	0.814	0.548	1.0000000
Gbp9	0.0002674	3.3944098	0.283	0.068	1.0000000
Phf11d	0.0002699	1.8343718	0.442	0.192	1.0000000
Parp9	0.0002977	3.1895987	0.389	0.164	1.0000000
BC005537	0.0003186	1.5327808	0.566	0.329	1.0000000
Parp14	0.0003618	1.7364523	0.531	0.288	1.0000000
Etnk1	0.0003639	1.0706114	0.575	0.315	1.0000000
Cacna2d3	0.0003645	2.8377693	0.212	0.027	1.0000000
Bglap3	0.0004380	1.7114147	0.186	0.014	1.0000000
Gvin-ps7	0.0004522	2.0859611	0.558	0.342	1.0000000
Slc25a23	0.0004737	1.6030931	0.301	0.082	1.0000000
Eif2ak2	0.0004816	1.3339524	0.779	0.616	1.0000000
Pim1	0.0005341	1.0745068	0.310	0.096	1.0000000
Fcgr1	0.0005507	0.5304902	0.850	0.685	1.0000000
Syngr1	0.0005960	-0.8745693	0.611	0.753	1.0000000
Oasl1	0.0006350	3.6416291	0.177	0.014	1.0000000
Yeats2	0.0006850	1.0615890	0.434	0.164	1.0000000
Usp12	0.0007114	-1.7635080	0.212	0.425	1.0000000
Or4m1	0.0007203	0.8873351	0.558	0.288	1.0000000
Ddx60	0.0007856	3.2313260	0.381	0.178	1.0000000
Rpl27rt	0.0007948	1.1872376	0.407	0.164	1.0000000
Dhx58	0.0008764	2.2083221	0.398	0.192	1.0000000
Tbc1d17	0.0008837	-1.9752687	0.212	0.438	1.0000000
Rdh14	0.0009081	2.5239321	0.221	0.041	1.0000000
Hspa4	0.0009162	1.5970181	0.319	0.110	1.0000000
Sass6	0.0009514	3.0759238	0.779	0.616	1.0000000
Mmp12	0.0009588	1.2198362	0.575	0.315	1.0000000
Smg9	0.0009894	2.7966054	0.451	0.233	1.0000000
Zfp12	0.0011424	4.3757188	0.274	0.082	1.0000000
Cmtm8	0.0011483	-3.4758316	0.088	0.260	1.0000000
Mtmr12	0.0012256	0.0965453	0.124	0.329	1.0000000
Ndufb2	0.0012750	2.6197800	0.513	0.315	1.0000000
Cnga3	0.0012920	1.4220726	0.319	0.110	1.0000000
Prkcd	0.0013160	0.6385280	0.717	0.493	1.0000000

within cluster Wt vs WT Stroke

[1] “Microglia0” [1] “Microglia2” [1] “Microglia3” [1] “no significant GO terms identified” [1] “Microglia5” [1] “Microglia4” [1] “no significant genes identified” [1] “Microglia1”

within cluster APPPS1_Stroke vs WT Stroke

[1] “Microglia0” [1] “no significant GO terms identified” [1] “Microglia2” [1] “Microglia3” [1] “no significant genes identified” [1] “Microglia5” [1] “no significant GO terms identified” [1] “Microglia4” [1] “no significant genes identified” [1] “Microglia1” [1] “no significant GO terms identified”

within cluster APPPS1 vs APPPS1 Stroke

[1] “Microglia0” [1] “Microglia2” [1] “no significant GO terms identified” [1] “Microglia3” [1] “no significant genes identified” [1] “Microglia5” [1] “Microglia4” [1] “no significant genes identified” [1] “Microglia1” [1] “no significant GO terms identified”

            used   (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells  18853959 1007.0   31936005 1705.6  31936005 1705.6
Vcells 371907655 2837.5  731145388 5578.2 731145388 5578.2

Pseudotime analysis

slinghsot starting Microglia 0

Past versions of fig.width==7-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

[1] "slingPseudotime_1"
[1] "slingPseudotime_2"
[1] "slingPseudotime_3"

Look for genes that are up/down-regulated along pseudotime, for the re-clustered cells (Same paper Fig 2G/H)

Trajectory genes

By default, estimates of the spline coefficients are not returned as they are difficult to interpret. Rather, a log-fold change of expression along each path is estimated to provide some indication of the overall magnitude and direction of any change.

Past versions of unnamed-chunk-110-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

# WGCNA

In the paper https://www.nature.com/articles/s41586-018-0023-4 this analysis was used to generate different modules of gene lists that can then be mapped onto different treatment/genotypes within one experiment (see Figure 4). This is an analysis that can be done in Seurat https://smorabit.github.io/tutorials/9_scWGCNA_tutorial/ Which could be very cool for our data. In the paper they also have 3 different conditions in 2 genotypes.

avoid running this section as it takes very long

Allowing parallel execution with up to 7 working processes.

pickSoftThreshold: will use block size 5277.
 pickSoftThreshold: calculating connectivity for given powers...
   ..working on genes 1 through 5277 of 8478
   ..working on genes 5278 through 8478 of 8478
   Power SFT.R.sq slope truncated.R.sq  mean.k. median.k. max.k.
1      1    0.884 -3.75          0.909 1.80e+02  1.63e+02 547.00
2      2    0.991 -2.51          0.996 8.15e+00  5.34e+00  93.20
3      3    0.976 -1.77          0.989 8.13e-01  2.36e-01  27.00
4      4    0.970 -1.47          0.990 1.75e-01  1.29e-02  12.80
5      5    0.940 -1.37          0.947 6.30e-02  8.42e-04   8.21
6      6    0.939 -1.30          0.938 3.02e-02  6.34e-05   6.00
7      7    0.970 -1.24          0.970 1.72e-02  5.37e-06   4.53
8      8    0.965 -1.20          0.956 1.10e-02  4.89e-07   3.50
9      9    0.427 -1.52          0.339 7.66e-03  4.85e-08   3.00
10    10    0.381 -1.73          0.273 5.70e-03  5.17e-09   3.00
11    12    0.433 -2.11          0.346 3.65e-03  6.21e-11   3.00
12    14    0.483 -2.22          0.358 2.70e-03  8.29e-13   3.00
13    16    0.518 -2.21          0.381 2.21e-03  1.15e-14   3.00
14    18    0.550 -2.16          0.483 1.93e-03  2.22e-16   3.00
15    20    0.568 -2.11          0.522 1.76e-03  0.00e+00   3.00

Past versions of unnamed-chunk-113-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

$nSets
[1] 1

$nGenes
[1] 8478

$nSamples
[1] 2944

$structureOK
[1] TRUE

 Calculating consensus modules and module eigengenes block-wise from all genes
 Calculating topological overlaps block-wise from all genes
   Flagging genes and samples with too many missing values...
    ..step 1
    TOM calculation: adjacency..
    ..will use 7 parallel threads.
     Fraction of slow calculations: 0.000000
    ..connectivity..
    ..matrix multiplication (system BLAS)..
    ..normalization..
    ..done.
 ..Working on block 1 .
 ..Working on block 1 .
 ..merging consensus modules that are too close..

## WGCNA by Genotype_treatment

WGCNA violin by condition

WGCNA violin by cluster

WGCNA Heatmap by condition

# A tibble: 20 × 10
# Groups:   variable, Treatment [10]
   variable    Treatment Genotype avg_Eigenmodule sd_Eigenvalue med_Eigenvalue
   <fct>       <chr>     <fct>              <dbl>         <dbl>          <dbl>
 1 MEyellow    Ctrl      WT             -0.00766        0.0186       -0.00179 
 2 MEyellow    Ctrl      APPPS1          0.00710        0.0146        0.0101  
 3 MEyellow    Stroke    WT             -0.00135        0.0187        0.00462 
 4 MEyellow    Stroke    APPPS1          0.00213        0.0184        0.00712 
 5 MEblue      Ctrl      WT              0.00759        0.0289       -0.00157 
 6 MEblue      Ctrl      APPPS1         -0.00337        0.00721      -0.00422 
 7 MEblue      Stroke    WT             -0.00330        0.00616      -0.00396 
 8 MEblue      Stroke    APPPS1         -0.00209        0.0165       -0.00447 
 9 MEbrown     Ctrl      WT              0.00370        0.0239        0.000574
10 MEbrown     Ctrl      APPPS1         -0.00555        0.0139       -0.00445 
11 MEbrown     Stroke    WT              0.00261        0.0170        0.00262 
12 MEbrown     Stroke    APPPS1         -0.000289       0.0147       -0.00115 
13 MEturquoise Ctrl      WT              0.00368        0.0235       -0.00402 
14 MEturquoise Ctrl      APPPS1         -0.00121        0.0159       -0.00438 
15 MEturquoise Stroke    WT             -0.00206        0.0126       -0.00364 
16 MEturquoise Stroke    APPPS1         -0.00109        0.0185       -0.00596 
17 MEgrey      Ctrl      WT             -0.00266        0.0220       -0.000564
18 MEgrey      Ctrl      APPPS1          0.00657        0.0153        0.00957 
19 MEgrey      Stroke    WT             -0.00456        0.0169       -0.000205
20 MEgrey      Stroke    APPPS1         -0.000372       0.0161        0.00324 
# ℹ 4 more variables: pval <dbl>, pval_ast <chr>, Genotype_Treatment <fct>,
#   Module <chr>

png 
  2 

WGCNA Heatmap by cluster

# A tibble: 30 × 8
# Groups:   variable [5]
   variable labels     avg_Eigenmodule sd_Eigenvalue med_Eigenvalue      pval
   <fct>    <fct>                <dbl>         <dbl>          <dbl>     <dbl>
 1 MEyellow Microglia0         0.00402       0.0114        0.00595  1.19e-274
 2 MEyellow Microglia1        -0.00465       0.0179        0.000574 1.19e-274
 3 MEyellow Microglia2         0.00968       0.0114        0.0123   1.19e-274
 4 MEyellow Microglia3        -0.0359        0.0267       -0.0405   1.19e-274
 5 MEyellow Microglia4         0.00616       0.0106        0.00890  1.19e-274
 6 MEyellow Microglia5         0.00899       0.00909       0.00926  1.19e-274
 7 MEblue   Microglia0        -0.00124       0.00781      -0.00321  5.28e- 91
 8 MEblue   Microglia1        -0.00129       0.0137       -0.00412  5.28e- 91
 9 MEblue   Microglia2        -0.00408       0.00551      -0.00465  5.28e- 91
10 MEblue   Microglia3         0.0247        0.0550       -0.00163  5.28e- 91
# ℹ 20 more rows
# ℹ 2 more variables: pval_ast <chr>, Module <chr>

png 
  2 

Past versions of unnamed-chunk-121-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Heatmaps Genewise per module

Heatmpas top 50 genes per module Conditions wise

Past versions of unnamed-chunk-123-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

[1] "blue"      "brown"     "grey"      "turquoise" "yellow"   

png 
  2 

png 
  2 

png 
  2 

png 
  2 

Heatmpas top 50 genes per module Cluster wise

[1] "blue"      "brown"     "grey"      "turquoise" "yellow"   

png 
  2 

png 
  2 

png 
  2 

png 
  2 

WGCNA GO terms

Exdendet Plots and DAta inspection

Dot plot showing top markers for condition clusters, same paper Fig 2f

MG related genes

Spatial_mutual genes

Custom Genes

cell cylce scoring plots

Past versions of unnamed-chunk-138-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

    Pairwise comparisons using t tests with pooled SD 

data:  metadata$S.Score and metadata$labels 

           Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
Microglia1 1          -          -          -          -         
Microglia2 1          1          -          -          -         
Microglia3 1          1          1          -          -         
Microglia4 1          1          1          1          -         
Microglia5 1          1          1          1          1         

P value adjustment method: holm 

    Pairwise comparisons using t tests with pooled SD 

data:  metadata$G2M.Score and metadata$labels 

           Microglia0 Microglia1 Microglia2 Microglia3 Microglia4
Microglia1 1          -          -          -          -         
Microglia2 1          1          -          -          -         
Microglia3 1          1          1          -          -         
Microglia4 1          1          1          1          -         
Microglia5 1          1          1          1          1         

P value adjustment method: holm 

Additonal Microglia subtype scores

Past versions of unnamed-chunk-144-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Additional QC plots final dataset

Past versions of unnamed-chunk-145-1.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Past versions of unnamed-chunk-145-2.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Past versions of unnamed-chunk-145-3.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

Past versions of unnamed-chunk-145-4.png

Version	Author	Date
0d6e2cb	achiocch	2026-03-18

            used (Mb) gc trigger   (Mb)  max used   (Mb)
Ncells  18123934  968   31936005 1705.6  31936005 1705.6
Vcells 301461451 2300  880494468 6717.7 880494468 6717.7

Session information

R version 4.4.0 (2024-04-24)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Etc/UTC
tzcode source: system (glibc)

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
 [1] TSCAN_1.44.0                ggbeeswarm_0.7.2           
 [3] chisq.posthoc.test_0.1.2    gprofiler2_0.2.3           
 [5] mclust_6.1.2                future_1.67.0              
 [7] ensembldb_2.30.0            AnnotationFilter_1.30.0    
 [9] GenomicFeatures_1.58.0      lm.beta_1.7-3              
[11] DESeq2_1.46.0               pheatmap_1.0.13            
[13] RColorBrewer_1.1-3          kableExtra_1.4.0           
[15] ggrepel_0.9.5               knitr_1.50                 
[17] org.Mm.eg.db_3.20.0         AnnotationDbi_1.68.0       
[19] plotly_4.11.0               WGCNA_1.74                 
[21] fastcluster_1.3.0           dynamicTreeCut_1.63-1      
[23] AnnotationHub_3.14.0        BiocFileCache_2.14.0       
[25] dbplyr_2.5.1                RCurl_1.98-1.17            
[27] clustree_0.5.1              ggraph_2.2.2               
[29] ggpubr_0.6.1                slingshot_2.14.0           
[31] TrajectoryUtils_1.14.0      SingleCellExperiment_1.28.1
[33] princurve_2.1.6             DT_0.34.0                  
[35] viridis_0.6.5               viridisLite_0.4.2          
[37] openxlsx_4.2.8              compareGroups_4.10.0       
[39] data.table_1.17.8           SingleR_2.8.0              
[41] SummarizedExperiment_1.36.0 Biobase_2.66.0             
[43] GenomicRanges_1.58.0        GenomeInfoDb_1.42.3        
[45] IRanges_2.40.1              S4Vectors_0.44.0           
[47] BiocGenerics_0.52.0         MatrixGenerics_1.18.1      
[49] matrixStats_1.5.0           harmony_1.2.3              
[51] Rcpp_1.1.0                  scCustomize_3.2.4          
[53] Seurat_5.3.0                SeuratObject_5.2.0         
[55] sp_2.2-0                    lubridate_1.9.4            
[57] forcats_1.0.1               stringr_1.5.2              
[59] dplyr_1.1.4                 purrr_1.1.0                
[61] readr_2.1.5                 tidyr_1.3.1                
[63] tibble_3.3.0                ggplot2_4.0.0              
[65] tidyverse_2.0.0             workflowr_1.7.2            

loaded via a namespace (and not attached):
  [1] igraph_2.1.4              ica_1.0-3                
  [3] Formula_1.2-5             scater_1.34.1            
  [5] rematch2_2.1.2            zlibbioc_1.52.0          
  [7] tidyselect_1.2.1          bit_4.6.0                
  [9] doParallel_1.0.17         BWStest_0.2.3            
 [11] lattice_0.22-7            rjson_0.2.23             
 [13] EnhancedVolcano_1.24.0    blob_1.3.0               
 [15] S4Arrays_1.6.0            parallel_4.4.0           
 [17] dichromat_2.0-0.1         png_0.1-9                
 [19] cli_3.6.5                 ProtGenerics_1.38.0      
 [21] askpass_1.2.1             openssl_2.3.4            
 [23] goftest_1.2-3             BiocIO_1.16.0            
 [25] textshaping_1.0.3         glmGamPoi_1.18.0         
 [27] bluster_1.16.0            officer_0.7.0            
 [29] BiocNeighbors_2.0.1       uwot_0.2.3               
 [31] curl_7.0.0                mime_0.13                
 [33] evaluate_1.0.5            stringi_1.8.7            
 [35] backports_1.5.0           PMCMRplus_1.9.12         
 [37] XML_3.99-0.19             httpuv_1.6.16            
 [39] paletteer_1.7.0           magrittr_2.0.4           
 [41] rappdirs_0.3.4            splines_4.4.0            
 [43] sctransform_0.4.2         HDF5Array_1.34.0         
 [45] DBI_1.2.3                 jquerylib_0.1.4          
 [47] withr_3.0.2               git2r_0.36.2             
 [49] reformulas_0.4.1          systemfonts_1.3.1        
 [51] rprojroot_2.1.1           lmtest_0.9-40            
 [53] tidygraph_1.3.1           rtracklayer_1.66.0       
 [55] BiocManager_1.30.26       htmlwidgets_1.6.4        
 [57] fs_1.6.6                  SuppDists_1.1-9.9        
 [59] labeling_0.4.3            SparseArray_1.6.2        
 [61] truncnorm_1.0-9           reticulate_1.43.0        
 [63] zoo_1.8-14                XVector_0.46.0           
 [65] UCSC.utils_1.2.0          RhpcBLASctl_0.23-42      
 [67] timechange_0.3.0          foreach_1.5.2            
 [69] caTools_1.18.3            patchwork_1.3.2          
 [71] grid_4.4.0                rhdf5_2.50.2             
 [73] pan_1.9                   RSpectra_0.16-2          
 [75] irlba_2.3.5.1             ggrastr_1.0.2            
 [77] alabaster.schemas_1.6.0   fastDummies_1.7.5        
 [79] lazyeval_0.2.2            yaml_2.3.10              
 [81] survival_3.8-3            scattermore_1.2          
 [83] BiocVersion_3.20.0        crayon_1.5.3             
 [85] RcppAnnoy_0.0.22          progressr_0.16.0         
 [87] tweenr_2.0.3              later_1.4.4              
 [89] ggridges_0.5.7            codetools_0.2-20         
 [91] base64enc_0.1-3           GlobalOptions_0.1.2      
 [93] KEGGREST_1.46.0           Rtsne_0.17               
 [95] shape_1.4.6.1             fastICA_1.2-7            
 [97] limma_3.62.2              Rsamtools_2.22.0         
 [99] gdtools_0.4.3             filelock_1.0.3           
[101] foreign_0.8-90            pkgconfig_2.0.3          
[103] xml2_1.4.0                spatstat.univar_3.1-4    
[105] GenomicAlignments_1.42.0  getPass_0.2-4            
[107] alabaster.base_1.6.1      spatstat.sparse_3.1-0    
[109] xtable_1.8-4              car_3.1-3                
[111] plyr_1.8.9                httr_1.4.7               
[113] rbibutils_2.3             tools_4.4.0              
[115] globals_0.18.0            beeswarm_0.4.0           
[117] htmlTable_2.4.3           broom_1.0.10             
[119] checkmate_2.3.3           nlme_3.1-168             
[121] ExperimentHub_2.14.0      crosstalk_1.2.2          
[123] lme4_1.1-37               digest_0.6.37            
[125] numDeriv_2016.8-1.1       bookdown_0.45            
[127] Matrix_1.7-4              farver_2.1.2             
[129] tzdb_0.5.0                reshape2_1.4.4           
[131] rpart_4.1.24              glue_1.8.0               
[133] mice_3.18.0               cachem_1.1.0             
[135] polyclip_1.10-7           Hmisc_5.2-4              
[137] generics_0.1.4            Biostrings_2.74.1        
[139] mvtnorm_1.3-3             presto_1.0.0             
[141] parallelly_1.45.1         statmod_1.5.0            
[143] impute_1.80.0             RcppHNSW_0.6.0           
[145] ragg_1.5.0                ScaledMatrix_1.14.0      
[147] fontBitstreamVera_0.1.1   carData_3.0-5            
[149] minqa_1.2.8               pbapply_1.7-4            
[151] httr2_1.2.1               glmnet_4.1-10            
[153] spam_2.11-1               dqrng_0.4.1              
[155] utf8_1.2.6                gtools_3.9.5             
[157] graphlayouts_1.2.2        alabaster.se_1.6.0       
[159] preprocessCore_1.68.0     ggsignif_0.6.4           
[161] gridExtra_2.3             shiny_1.11.1             
[163] GenomeInfoDbData_1.2.13   rhdf5filters_1.18.1      
[165] memoise_2.0.1             rmarkdown_2.30           
[167] scales_1.4.0              gypsum_1.2.0             
[169] svglite_2.2.1             RANN_2.6.2               
[171] fontLiberation_0.1.0      spatstat.data_3.1-8      
[173] rstudioapi_0.17.1         cluster_2.1.8.1          
[175] whisker_0.4.1             janitor_2.2.1            
[177] spatstat.utils_3.2-0      hms_1.1.4                
[179] fitdistrplus_1.2-4        cowplot_1.2.0            
[181] colorspace_2.1-2          rlang_1.1.7              
[183] jomo_2.7-6                Rsolnp_2.0.1             
[185] DelayedMatrixStats_1.28.1 sparseMatrixStats_1.18.0 
[187] dotCall64_1.2             scuttle_1.16.0           
[189] ggforce_0.5.0             circlize_0.4.16          
[191] mgcv_1.9-3                xfun_0.53                
[193] multcompView_0.1-10       alabaster.matrix_1.6.1   
[195] iterators_1.0.14          abind_1.4-8              
[197] celldex_1.16.0            gmp_0.7-5                
[199] Rhdf5lib_1.28.0           bitops_1.0-9             
[201] Rdpack_2.6.4              ps_1.9.1                 
[203] promises_1.3.3            RSQLite_2.4.3            
[205] DelayedArray_0.32.0       Rmpfr_1.1-1              
[207] compiler_4.4.0            alabaster.ranges_1.6.0   
[209] boot_1.3-32               writexl_1.5.4            
[211] beachmat_2.22.0           listenv_0.9.1            
[213] edgeR_4.4.2               fontquiver_0.2.1         
[215] BiocSingular_1.22.0       tensor_1.5.1             
[217] MASS_7.3-65               kSamples_1.2-12          
[219] uuid_1.2-1                BiocParallel_1.40.2      
[221] spatstat.random_3.4-2     R6_2.6.1                 
[223] fastmap_1.2.0             rstatix_0.7.2            
[225] vipor_0.4.7               ROCR_1.0-11              
[227] mcprogress_0.1.1          rsvd_1.0.5               
[229] mitml_0.4-5               nnet_7.3-20              
[231] gtable_0.3.6              KernSmooth_2.23-26       
[233] miniUI_0.1.2              deldir_2.0-4             
[235] htmltools_0.5.8.1         bit64_4.6.0-1            
[237] spatstat.explore_3.5-3    lifecycle_1.0.5          
[239] ggprism_1.0.7             HardyWeinberg_1.7.9      
[241] S7_0.2.0                  zip_2.3.3                
[243] processx_3.8.6            restfulr_0.0.16          
[245] nloptr_2.2.1              callr_3.7.6              
[247] sass_0.4.10               vctrs_0.7.1              
[249] isoband_0.2.7             flextable_0.9.10         
[251] spatstat.geom_3.6-0       snakecase_0.11.1         
[253] scran_1.34.0              future.apply_1.20.0      
[255] bslib_0.9.0               pillar_1.11.1            
[257] gplots_3.2.0              rmdformats_1.0.4         
[259] metapod_1.14.0            combinat_0.0-8           
[261] locfit_1.5-9.12           jsonlite_2.0.0           
[263] chron_2.3-62