B cells
Chih-Hsuan Wu
Last updated: 2024-10-19
Checks: 7 0
Knit directory: DEanalysis/
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| html | 9bd93f2 | C-HW | 2024-10-19 | Build site. |
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| html | fc4ab47 | C-HW | 2023-08-03 | data2 results |
Data summary
Number of DEGs from each method
Upset plot
Volcano plot
Histogram of p-value/adj.p-value
P-Value comparison across different methods
Log2 fold change comparison across different methods
Violin plot of log2mean of DEGs
Violin plot of gene expression frequency of DEGs
Heatmap of top DEGs
Additional DEGs from other methods
pb-DESeq2
MA plot
Enrichment analysis
Poisson-glmm DEGs
All DEGs
Up-regulated DEGs
Down-regulated DEGs
| Version | Author | Date |
|---|---|---|
| 9bd93f2 | C-HW | 2024-10-19 |
| 4602dd7 | C-HW | 2024-10-14 |
| a0d4555 | C-HW | 2023-12-15 |
| 2a17159 | C-HW | 2023-12-05 |
| 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 |
pb-DESeq2 DEGs
All DEGs
Up-regulated DEGs
MMpoisson DEGs
All DEGs
Up-regulated DEGs
Down-regulated DEGs
R version 4.4.1 (2024-06-14)
Platform: x86_64-apple-darwin20
Running under: macOS Monterey 12.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/Chicago
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] UpSetR_1.4.0 SeuratObject_5.0.2
[3] sp_2.1-4 pathview_1.44.0
[5] org.Hs.eg.db_3.19.1 AnnotationDbi_1.66.0
[7] enrichplot_1.24.4 clusterProfiler_4.12.6
[9] reshape_0.8.9 gridExtra_2.3
[11] pheatmap_1.0.12 SingleCellExperiment_1.26.0
[13] SummarizedExperiment_1.34.0 Biobase_2.64.0
[15] GenomicRanges_1.56.2 GenomeInfoDb_1.40.1
[17] IRanges_2.38.1 S4Vectors_0.42.1
[19] BiocGenerics_0.50.0 MatrixGenerics_1.16.0
[21] matrixStats_1.4.1 ggpubr_0.6.0
[23] dplyr_1.1.4 ggplot2_3.5.1
loaded via a namespace (and not attached):
[1] splines_4.4.1 later_1.3.2 bitops_1.0-9
[4] ggplotify_0.1.2 tibble_3.2.1 R.oo_1.26.0
[7] polyclip_1.10-7 graph_1.82.0 XML_3.99-0.17
[10] lifecycle_1.0.4 httr2_1.0.5 rstatix_0.7.2
[13] rprojroot_2.0.4 globals_0.16.3 lattice_0.22-6
[16] MASS_7.3-61 backports_1.5.0 magrittr_2.0.3
[19] sass_0.4.9 rmarkdown_2.28 jquerylib_0.1.4
[22] yaml_2.3.10 httpuv_1.6.15 spam_2.11-0
[25] cowplot_1.1.3 DBI_1.2.3 RColorBrewer_1.1-3
[28] abind_1.4-8 zlibbioc_1.50.0 purrr_1.0.2
[31] R.utils_2.12.3 ggraph_2.2.1 RCurl_1.98-1.16
[34] yulab.utils_0.1.7 tweenr_2.0.3 rappdirs_0.3.3
[37] git2r_0.33.0 GenomeInfoDbData_1.2.12 ggrepel_0.9.6
[40] listenv_0.9.1 tidytree_0.4.6 parallelly_1.38.0
[43] codetools_0.2-20 DelayedArray_0.30.1 DOSE_3.30.5
[46] ggforce_0.4.2 tidyselect_1.2.1 aplot_0.2.3
[49] UCSC.utils_1.0.0 farver_2.1.2 viridis_0.6.5
[52] jsonlite_1.8.9 progressr_0.14.0 tidygraph_1.3.1
[55] Formula_1.2-5 ggnewscale_0.5.0 tools_4.4.1
[58] treeio_1.28.0 Rcpp_1.0.13 glue_1.8.0
[61] SparseArray_1.4.8 xfun_0.48 qvalue_2.36.0
[64] withr_3.0.1 fastmap_1.2.0 fansi_1.0.6
[67] digest_0.6.37 R6_2.5.1 gridGraphics_0.5-1
[70] colorspace_2.1-1 GO.db_3.19.1 RSQLite_2.3.7
[73] R.methodsS3_1.8.2 utf8_1.2.4 tidyr_1.3.1
[76] generics_0.1.3 data.table_1.16.2 graphlayouts_1.2.0
[79] httr_1.4.7 S4Arrays_1.4.1 scatterpie_0.2.4
[82] whisker_0.4.1 pkgconfig_2.0.3 gtable_0.3.5
[85] blob_1.2.4 workflowr_1.7.1 XVector_0.44.0
[88] shadowtext_0.1.4 htmltools_0.5.8.1 carData_3.0-5
[91] dotCall64_1.2 fgsea_1.30.0 scales_1.3.0
[94] png_0.1-8 ggfun_0.1.6 knitr_1.48
[97] rstudioapi_0.16.0 reshape2_1.4.4 nlme_3.1-166
[100] cachem_1.1.0 stringr_1.5.1 parallel_4.4.1
[103] pillar_1.9.0 grid_4.4.1 vctrs_0.6.5
[106] promises_1.3.0 car_3.1-3 Rgraphviz_2.48.0
[109] evaluate_1.0.1 KEGGgraph_1.64.0 cli_3.6.3
[112] compiler_4.4.1 rlang_1.1.4 crayon_1.5.3
[115] future.apply_1.11.2 ggsignif_0.6.4 labeling_0.4.3
[118] plyr_1.8.9 fs_1.6.4 stringi_1.8.4
[121] viridisLite_0.4.2 BiocParallel_1.38.0 munsell_0.5.1
[124] Biostrings_2.72.1 lazyeval_0.2.2 GOSemSim_2.30.2
[127] Matrix_1.7-0 patchwork_1.3.0 bit64_4.5.2
[130] future_1.34.0 KEGGREST_1.44.1 highr_0.11
[133] igraph_2.0.3 broom_1.0.7 memoise_2.0.1
[136] bslib_0.8.0 ggtree_3.12.0 fastmatch_1.1-4
[139] bit_4.5.0 ape_5.8 gson_0.1.0