Package: CDEnrich 0.99.1

Yushan Chen

CDEnrich: Enrichment Analysis for Cell Death Pathways

Provides a curated collection of gene sets for major cell death modalities, together with tools for over-representation analysis, gene set enrichment analysis, single-sample gene set enrichment analysis, differential pathway analysis, and visualization.

Authors:Yushan Chen [aut, cre]

CDEnrich_0.99.1.tar.gz
CDEnrich_0.99.1.zip(r-4.7-any)CDEnrich_0.99.1.zip(r-4.6-any)CDEnrich_0.99.1.zip(r-4.5-any)
CDEnrich_0.99.1.tgz(r-4.6-any)CDEnrich_0.99.1.tgz(r-4.5-any)
CDEnrich_0.99.1.tar.gz(r-4.7-any)CDEnrich_0.99.1.tar.gz(r-4.6-any)
CDEnrich_0.99.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CDEnrich/json (API)

# Install 'CDEnrich' in R:

install.packages('CDEnrich', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/yushan-chen-829/cdenrich/issues

Datasets:

cd_Genesets - Curated Cell Death Pathway Gene Sets
demo_all_genes - Demonstration Background Gene Universe
demo_deg - Demonstration DEG List for Single-Group ORA
demo_deg_list - Demonstration DEG Lists for Multi-Group ORA
demo_expr - Demonstration Expression Matrix for ssGSEA
demo_group - Demonstration Sample Groups for ssGSEA
demo_rank_apop - Demonstration Ranked Gene List for Single-Group GSEA
demo_rank_apop_list - Demonstration Ranked Gene Lists for Multi-Group GSEA
demo_targeted_deg - Demonstration DEG List for Targeted ORA
representative_genes - Representative Gene Sets for Cell Death Types
representative_pathways - Representative Pathway Recommendation Metadata

On CRAN:

genesetenrichment pathways geneexpression differentialexpression cellbiology

3.18 score 21 exports 162 dependencies

Last updated from:7976584a29. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	230
linux-devel	OK	463
source / vignettes	OK	287
linux-release	OK	439
macos-release	OK	309
macos-oldrel	OK	448
windows-devel	OK	285
windows-release	OK	365
windows-oldrel	OK	370
wasm-release	OK	183

Exports:celldeath_compare_enrich celldeath_enrich celldeath_gsea celldeath_gsea_multiple celldeath_ssgsea celldeath_ssgsea_diff get_representative_pathway load_cell_death_genes plot_death_compare_bubble plot_death_compare_heatmap plot_death_enrich_bubble plot_death_enrich_network plot_death_enrich_targeted plot_death_gsea_curve plot_death_gsea_curve_multiple plot_death_gsea_heatmap_multiple plot_death_gsea_ranked plot_death_ssgsea_bar plot_death_ssgsea_boxplot plot_death_ssgsea_heatmap plot_death_volcano

Dependencies:abind aisdk annotate AnnotationDbi ape aplot askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics biocmake BiocParallel Biostrings bit bit64 blob bslib cachem callr cli cluster clusterProfiler codetools cpp11 crayon curl DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry DOSE dplyr enrichit enrichplot evaluate farver fastmap filelock fontawesome fontBitstreamVera fontLiberation fontquiver formatR fs futile.logger futile.options gdtools generics GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim graph gridGraphics GSEABase gson GSVA gtable h5mread HDF5Array highr htmltools htmlwidgets httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lazyeval lifecycle magick magrittr MASS Matrix MatrixGenerics matrixStats memoise memuse mime nlme openssl otel patchwork pheatmap pillar pkgconfig plyr png polyclip processx ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppEigen reshape2 rhdf5 rhdf5filters Rhdf5lib rjson rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo SingleCellExperiment snow SparseArray sparseMatrixStats SpatialExperiment stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr utf8 vctrs viridisLite withr xfun XML xtable XVector yaml yulab.utils

CDEnrich: Complete Usage Guide for Cell Death Enrichment

Rendered fromCDEnrich-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-09-13
Started: 2026-09-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Curated Cell Death Pathway Gene Sets	cd_Genesets
CDEnrich Demonstration Data	CDEnrich_demo_data
Curated Data Included in CDEnrich	CDEnrich-data
ORA Enrichment Analysis for Cell Death Pathways (Multi-Group Comparison)	celldeath_compare_enrich
ORA Enrichment Analysis for Cell Death Pathways (Single Group)	celldeath_enrich
Cell Death Pathway GSEA Analysis	celldeath_gsea
Multiple Group Cell Death Pathway GSEA Analysis	celldeath_gsea_multiple
ssGSEA Analysis for Cell Death Pathways	celldeath_ssgsea
Differential Analysis of ssGSEA Scores Between Groups	celldeath_ssgsea_diff
Demonstration Background Gene Universe	demo_all_genes
Demonstration DEG List for Single-Group ORA	demo_deg
Demonstration DEG Lists for Multi-Group ORA	demo_deg_list
Demonstration Expression Matrix for ssGSEA	demo_expr
Demonstration Sample Groups for ssGSEA	demo_group
Demonstration Ranked Gene List for Single-Group GSEA	demo_rank_apop
Demonstration Ranked Gene Lists for Multi-Group GSEA	demo_rank_apop_list
Demonstration DEG List for Targeted ORA	demo_targeted_deg
Get the Recommended Representative Gene Set for a Cell Death Type	get_representative_pathway
Load Curated Cell Death Gene Sets	load_cell_death_genes
Visualization of Multi-Group Cell Death Enrichment Comparison	plot_death_compare_bubble
Visualization of Multi-Group Cell Death Enrichment Comparison (Heatmap)	plot_death_compare_heatmap
Visualization of Cell Death Enrichment Results (Bubble Plot)	plot_death_enrich_bubble
Visualization of Cell Death Enrichment Results (Enrichment Network)	plot_death_enrich_network
Targeted Single-Pathway ORA Summary Plot	plot_death_enrich_targeted
Plot GSEA Curve for Cell Death Pathways	plot_death_gsea_curve
Plot GSEA Curves for Multiple Group Cell Death Pathways	plot_death_gsea_curve_multiple
Heatmap for Multi-Group GSEA Results	plot_death_gsea_heatmap_multiple
Plot GSEA Ranking Score Curve for Cell Death Pathways	plot_death_gsea_ranked
Visualization of Cell Death ssGSEA Scores (Mean Barplot)	plot_death_ssgsea_bar
Visualization of Cell Death ssGSEA Scores (Grouped Boxplot)	plot_death_ssgsea_boxplot
Visualization of Cell Death ssGSEA Scores (Heatmap)	plot_death_ssgsea_heatmap
Volcano Plot for Cell Death Enrichment Results	plot_death_volcano
Print Method for celldeath_ssgsea Objects	print.celldeath_ssgsea
Representative Gene Sets for Cell Death Types	representative_genes
Representative Pathway Recommendation Metadata	representative_pathways