- Data summary
- Number of hits from each method
- Volcano plot
- Histogram of p-value/adj.p-value
- Violin plot of log2mean of DEGs
- Violin plot of gene expression frequency of DEGs
- Heatmap of top DEGs
- Poisson-glmm DEGs
- Additional DEGs from other methods
- pb-DESeq2
- MA plot
- Enrichment analysis
- GO object (all)
- GO object (positive)
- GO object (negative)
B cells
Chih-Hsuan Wu
Last updated: 2023-11-30
Checks: 5 2
Knit directory: DEanalysis/
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Data summary
Number of hits from each method
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 |
|---|---|---|
| d7d838c | C-HW | 2023-08-11 |
Heatmap of top DEGs
MA plot
Enrichment analysis
GO object (positive)
GO object (negative)
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_0.39
[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_1.1.1
[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_0.21
[73] stringr_1.5.0 fastmap_1.1.1 yaml_2.3.7
[76] ggtree_3.6.2 knitr_1.27 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_1.7.12
[97] highr_0.10 lattice_0.21-8 Matrix_1.5-4.1
[100] vctrs_0.6.3 pillar_1.9.0 lifecycle_1.0.3
[103] jquerylib_0.1.4 data.table_1.14.8 cowplot_1.1.1
[106] bitops_1.0-7 httpuv_1.6.11 patchwork_1.1.2
[109] qvalue_2.30.0 R6_2.5.1 promises_1.2.0.1
[112] codetools_0.2-19 MASS_7.3-60 rprojroot_2.0.3
[115] withr_2.5.0 GenomeInfoDbData_1.2.9 parallel_4.2.2
[118] grid_4.2.2 ggfun_0.1.1 tidyr_1.3.0
[121] HDO.db_0.99.1 rmarkdown_2.23 carData_3.0-5
[124] ggnewscale_0.4.9 git2r_0.32.0 ggforce_0.4.1