Last updated: 2023-12-05

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Knit directory: DEanalysis/

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File Version Author Date Message
html bc13544 C-HW 2023-12-04 Build site.
Rmd 39196a3 C-HW 2023-12-04 fix log2FC sign
html 9e46095 C-HW 2023-12-04 Build site.
Rmd 1a9175a C-HW 2023-12-04 fix up-regulated/down-regulated order
html 917ddb4 C-HW 2023-12-03 Build site.
Rmd 6ef5f9b C-HW 2023-12-03 wflow_publish("analysis/Bcells.Rmd")
html 35e3430 C-HW 2023-12-03 Build site.
Rmd cc79a4b C-HW 2023-12-03 up-regulated/ down-regulated
html 42900f0 C-HW 2023-12-01 Build site.
Rmd c774a2d C-HW 2023-12-01 modify method title
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html 3d93462 C-HW 2023-12-01 Build site.
Rmd 3be1a6b C-HW 2023-12-01 wflow_publish("analysis/Bcells.Rmd")
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Rmd c75b0bf C-HW 2023-12-01 wflow_publish("analysis/Bcells.Rmd")
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Rmd 3803697 C-HW 2023-12-01 upload rmd
html eeb5d79 C-HW 2023-11-30 update B cells and data2
html 85fc2fe C-HW 2023-09-12 update
html d7d838c C-HW 2023-08-11 update graph
html 382e3cd C-HW 2023-08-03 update data2 heatmap
html fc4ab47 C-HW 2023-08-03 data2 results

Data summary

Version Author Date
3d93462 C-HW 2023-12-01
632be33 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
85fc2fe C-HW 2023-09-12
d7d838c C-HW 2023-08-11
fc4ab47 C-HW 2023-08-03

Number of DEGs from each method

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42900f0 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
d7d838c C-HW 2023-08-11
fc4ab47 C-HW 2023-08-03

To compare the results fairly, the genes displayed in all of the plots below are restricted to the inputs of pois_glmm. That is, the genes not containing in the inputs of pois_glmm are excluded.

Version Author Date
42900f0 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
d7d838c C-HW 2023-08-11

Volcano plot

Version Author Date
bc13544 C-HW 2023-12-04
42900f0 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
d7d838c C-HW 2023-08-11
fc4ab47 C-HW 2023-08-03

Histogram of p-value/adj.p-value

Version Author Date
42900f0 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
d7d838c C-HW 2023-08-11

Violin plot of log2mean of DEGs

Version Author Date
42900f0 C-HW 2023-12-01
3d93462 C-HW 2023-12-01
632be33 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
85fc2fe C-HW 2023-09-12
d7d838c C-HW 2023-08-11

Violin plot of gene expression frequency of DEGs

Version Author Date
42900f0 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30
d7d838c C-HW 2023-08-11

Heatmap of top DEGs

Poisson-glmm DEGs

Version Author Date
eeb5d79 C-HW 2023-11-30
85fc2fe C-HW 2023-09-12
d7d838c C-HW 2023-08-11

Additional DEGs from other methods

pb-DESeq2

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eeb5d79 C-HW 2023-11-30

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eeb5d79 C-HW 2023-11-30
85fc2fe C-HW 2023-09-12
d7d838c C-HW 2023-08-11
382e3cd C-HW 2023-08-03
fc4ab47 C-HW 2023-08-03

MA plot

Version Author Date
bc13544 C-HW 2023-12-04
42900f0 C-HW 2023-12-01
3d93462 C-HW 2023-12-01
632be33 C-HW 2023-12-01
85fc2fe C-HW 2023-09-12
d7d838c C-HW 2023-08-11
382e3cd C-HW 2023-08-03
fc4ab47 C-HW 2023-08-03

Enrichment analysis

Poisson-glmm DEGs

All DEGs

Version Author Date
3d93462 C-HW 2023-12-01
632be33 C-HW 2023-12-01
85fc2fe C-HW 2023-09-12
d7d838c C-HW 2023-08-11
fc4ab47 C-HW 2023-08-03

Version Author Date
bc13544 C-HW 2023-12-04
3d93462 C-HW 2023-12-01
84814ca C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30

Up-regulated DEGs

Version Author Date
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
3d93462 C-HW 2023-12-01

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
35e3430 C-HW 2023-12-03
3d93462 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30

Down-regulated DEGs

Version Author Date
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
3d93462 C-HW 2023-12-01

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
35e3430 C-HW 2023-12-03
42900f0 C-HW 2023-12-01
e3d28f8 C-HW 2023-12-01
3d93462 C-HW 2023-12-01
eeb5d79 C-HW 2023-11-30

pb-DESeq2 DEGs

All DEGs

Version Author Date
3d93462 C-HW 2023-12-01

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
35e3430 C-HW 2023-12-03
42900f0 C-HW 2023-12-01
e3d28f8 C-HW 2023-12-01
3d93462 C-HW 2023-12-01
84814ca C-HW 2023-12-01

Up-regulated DEGs

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
35e3430 C-HW 2023-12-03
3d93462 C-HW 2023-12-01

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
35e3430 C-HW 2023-12-03
42900f0 C-HW 2023-12-01
e3d28f8 C-HW 2023-12-01
3d93462 C-HW 2023-12-01
84814ca C-HW 2023-12-01

Down-regulated DEGs

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
35e3430 C-HW 2023-12-03

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
35e3430 C-HW 2023-12-03

MMpoisson DEGs

All DEGs

Version Author Date
35e3430 C-HW 2023-12-03

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
35e3430 C-HW 2023-12-03

Up-regulated DEGs

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
35e3430 C-HW 2023-12-03

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
917ddb4 C-HW 2023-12-03
35e3430 C-HW 2023-12-03

Down-regulated DEGs

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
35e3430 C-HW 2023-12-03

Version Author Date
bc13544 C-HW 2023-12-04
9e46095 C-HW 2023-12-04
35e3430 C-HW 2023-12-03

R version 4.2.2 (2022-10-31)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur ... 10.16

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] pathview_1.38.0             org.Hs.eg.db_3.16.0        
 [3] AnnotationDbi_1.60.2        enrichplot_1.18.4          
 [5] clusterProfiler_4.6.2       reshape_0.8.9              
 [7] gridExtra_2.3               pheatmap_1.0.12            
 [9] SingleCellExperiment_1.20.1 SummarizedExperiment_1.28.0
[11] Biobase_2.58.0              GenomicRanges_1.50.2       
[13] GenomeInfoDb_1.34.9         IRanges_2.32.0             
[15] S4Vectors_0.36.2            BiocGenerics_0.44.0        
[17] MatrixGenerics_1.10.0       matrixStats_1.0.0          
[19] ggpubr_0.6.0                dplyr_1.1.2                
[21] ggplot2_3.4.2              

loaded via a namespace (and not attached):
  [1] shadowtext_0.1.2       backports_1.4.1        fastmatch_1.1-3       
  [4] workflowr_1.7.0        plyr_1.8.8             igraph_1.5.0          
  [7] lazyeval_0.2.2         splines_4.2.2          BiocParallel_1.32.6   
 [10] digest_0.6.33          yulab.utils_0.0.6      htmltools_0.5.5       
 [13] GOSemSim_2.24.0        viridis_0.6.3          GO.db_3.16.0          
 [16] fansi_1.0.4            magrittr_2.0.3         memoise_2.0.1         
 [19] Biostrings_2.66.0      graphlayouts_1.0.0     colorspace_2.1-0      
 [22] blob_1.2.4             ggrepel_0.9.3          xfun_0.41             
 [25] crayon_1.5.2           RCurl_1.98-1.12        jsonlite_1.8.7        
 [28] graph_1.76.0           scatterpie_0.2.1       ape_5.7-1             
 [31] glue_1.6.2             polyclip_1.10-4        gtable_0.3.3          
 [34] zlibbioc_1.44.0        XVector_0.38.0         DelayedArray_0.24.0   
 [37] car_3.1-2              Rgraphviz_2.42.0       abind_1.4-5           
 [40] scales_1.2.1           DOSE_3.24.2            DBI_1.1.3             
 [43] rstatix_0.7.2          Rcpp_1.0.11            viridisLite_0.4.2     
 [46] gridGraphics_0.5-1     tidytree_0.4.4         bit_4.0.5             
 [49] httr_1.4.6             fgsea_1.24.0           RColorBrewer_1.1-3    
 [52] XML_3.99-0.14          pkgconfig_2.0.3        farver_2.1.1          
 [55] sass_0.4.7             utf8_1.2.3             labeling_0.4.2        
 [58] ggplotify_0.1.1        tidyselect_1.2.0       rlang_1.1.2           
 [61] reshape2_1.4.4         later_1.3.1            munsell_0.5.0         
 [64] tools_4.2.2            cachem_1.0.8           downloader_0.4        
 [67] cli_3.6.1              generics_0.1.3         RSQLite_2.3.1         
 [70] gson_0.1.0             broom_1.0.5            evaluate_0.23         
 [73] stringr_1.5.1          fastmap_1.1.1          yaml_2.3.7            
 [76] ggtree_3.6.2           knitr_1.29             bit64_4.0.5           
 [79] fs_1.6.3               tidygraph_1.2.3        purrr_1.0.1           
 [82] KEGGREST_1.38.0        ggraph_2.1.0           nlme_3.1-162          
 [85] whisker_0.4.1          KEGGgraph_1.58.3       aplot_0.1.10          
 [88] compiler_4.2.2         rstudioapi_0.15.0      png_0.1-8             
 [91] ggsignif_0.6.4         treeio_1.22.0          tibble_3.2.1          
 [94] tweenr_2.0.2           bslib_0.5.0            stringi_1.8.2         
 [97] lattice_0.21-8         Matrix_1.5-4.1         vctrs_0.6.4           
[100] pillar_1.9.0           lifecycle_1.0.4        jquerylib_0.1.4       
[103] data.table_1.14.8      cowplot_1.1.1          bitops_1.0-7          
[106] httpuv_1.6.11          patchwork_1.1.2        qvalue_2.30.0         
[109] R6_2.5.1               promises_1.2.0.1       codetools_0.2-19      
[112] MASS_7.3-60            rprojroot_2.0.3        withr_2.5.0           
[115] GenomeInfoDbData_1.2.9 parallel_4.2.2         grid_4.2.2            
[118] ggfun_0.1.1            tidyr_1.3.0            HDO.db_0.99.1         
[121] rmarkdown_2.23         carData_3.0-5          ggnewscale_0.4.9      
[124] git2r_0.32.0           ggforce_0.4.1