Last updated: 2023-12-10

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Knit directory: DEanalysis/

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File Version Author Date Message
Rmd ae4b56c C-HW 2023-12-10 adjust ylim of p-value histogram
html ac027b0 C-HW 2023-12-09 Build site.
Rmd 582be29 C-HW 2023-12-09 update new DE results
html 2a17159 C-HW 2023-12-05 Build site.
Rmd e7f3de4 C-HW 2023-12-05 fix Wilcox log2FC sign
html bc13544 C-HW 2023-12-04 Build site.
Rmd 39196a3 C-HW 2023-12-04 fix log2FC sign
html 42900f0 C-HW 2023-12-01 Build site.
Rmd c774a2d C-HW 2023-12-01 modify method title
Rmd 031d955 C-HW 2023-12-01 create t score comparison
html 031d955 C-HW 2023-12-01 create t score comparison
Rmd 3803697 C-HW 2023-12-01 upload rmd
html 5dcc60e C-HW 2023-11-29 updload again
html 59b08c2 C-HW 2023-11-29 update index, FD permuation, plots axes
html 91b404e C-HW 2023-11-29 update all pairs
html dc6ac7a C-HW 2023-11-29 update all pairs
html e8b0519 C-HW 2023-11-29 update all pairs
html 85fc2fe C-HW 2023-09-12 update
html d7d838c C-HW 2023-08-11 update graph
html 7ee9782 C-HW 2023-07-13 add 8_17
html ccb68e2 C-HW 2023-06-29 log2fc consistence
html 3121ffb C-HW 2023-06-22 color palette heatmap
html 366cd53 C-HW 2023-06-06 add group8_17&2_19

Data summary

Version Author Date
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Mean difference in raw data/normalized data

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031d955 C-HW 2023-12-01
59b08c2 C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Number of DEGs from each method

Version Author Date
ac027b0 C-HW 2023-12-09
42900f0 C-HW 2023-12-01
e8b0519 C-HW 2023-11-29

Volcano plot

Version Author Date
ac027b0 C-HW 2023-12-09
2a17159 C-HW 2023-12-05
bc13544 C-HW 2023-12-04
42900f0 C-HW 2023-12-01
e8b0519 C-HW 2023-11-29

Histogram of p-value/adj.p-value

Version Author Date
ac027b0 C-HW 2023-12-09
42900f0 C-HW 2023-12-01
e8b0519 C-HW 2023-11-29

P-Value comparison across different methods

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ac027b0 C-HW 2023-12-09
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Log2 fold change comparison across different methods

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ac027b0 C-HW 2023-12-09
91b404e C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Violin plot of log2mean of DEGs

Version Author Date
ac027b0 C-HW 2023-12-09
91b404e C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Violin plot of gene expression frequency of DEGs

Version Author Date
ac027b0 C-HW 2023-12-09
91b404e C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Heatmap of top DEGs

Poisson-glmm DEGs

UMI counts

Version Author Date
ac027b0 C-HW 2023-12-09
e8b0519 C-HW 2023-11-29

VST data

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ac027b0 C-HW 2023-12-09
e8b0519 C-HW 2023-11-29

CPM data

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ac027b0 C-HW 2023-12-09
59b08c2 C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Integrated data

Version Author Date
ac027b0 C-HW 2023-12-09
91b404e C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Additional DEGs from other methods

pb-DESeq2

Version Author Date
ac027b0 C-HW 2023-12-09
59b08c2 C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Binomial-glmm

Version Author Date
ac027b0 C-HW 2023-12-09
59b08c2 C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

MAST

Version Author Date
ac027b0 C-HW 2023-12-09
59b08c2 C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

MMpoisson

Version Author Date
ac027b0 C-HW 2023-12-09
59b08c2 C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

DEGs in Poisson-glmm not identified by MMpoisson

In the MMpoisson model, cell type is considered as a random effect. This approach treats certain aspects of cell type variations as random factors. Consequently, it may obscure the true variation in cell types, limiting its ability to accurately reveal the specific differences between different cell types.

Additionally, the library size is employed as an offset to normalize the counts. That is, the model is considering rate instead of counts. Suppose some genes are highly expressed in one cell type than the other, the absolute difference could be eliminate after accounting for library size. This normalization approach may inadvertently mask certain gene expression differences between cell types.

Version Author Date
ac027b0 C-HW 2023-12-09
2a17159 C-HW 2023-12-05
bc13544 C-HW 2023-12-04
42900f0 C-HW 2023-12-01
031d955 C-HW 2023-12-01
e8b0519 C-HW 2023-11-29

MA plot

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ac027b0 C-HW 2023-12-09
e8b0519 C-HW 2023-11-29

Enrichment analysis

GO object

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ac027b0 C-HW 2023-12-09

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ac027b0 C-HW 2023-12-09
91b404e C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

enrichKEGG object

Version Author Date
ac027b0 C-HW 2023-12-09
2a17159 C-HW 2023-12-05
bc13544 C-HW 2023-12-04
42900f0 C-HW 2023-12-01
5dcc60e C-HW 2023-11-29
59b08c2 C-HW 2023-11-29
91b404e C-HW 2023-11-29
dc6ac7a C-HW 2023-11-29
e8b0519 C-HW 2023-11-29

Version Author Date
ac027b0 C-HW 2023-12-09

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