Package: DSGEr 1.3.1
Pingwei Guo
DSGEr: Transcriptional Disruption Score for Gene Sets
Computes pathway-level transcriptional disruption scores from differential expression p-values using permutation tests with Generalized Pareto Distribution (GPD) tail extrapolation and false discovery rate (FDR) correction. Reference: Guo P, Li H (2026) DSGE: Disruption Score of Gene Expression for Gene-Set Enrichment Analysis. <https://github.com/LHJLab/DSGE>.
Authors:
DSGEr_1.3.1.tar.gz
DSGEr_1.3.1.tar.gz(r-4.7-arm64)DSGEr_1.3.1.tar.gz(r-4.7-x86_64)DSGEr_1.3.1.tar.gz(r-4.6-arm64)DSGEr_1.3.1.tar.gz(r-4.6-x86_64)
DSGEr_1.3.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
DSGEr/json (API)
| # Install 'DSGEr' in R: |
| install.packages('DSGEr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:b6bfdae8b5. Checks:6 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | OK | 205 | ||
| linux-devel-x86_64 | OK | 205 | ||
| source / vignettes | OK | 189 | ||
| linux-release-arm64 | OK | 218 | ||
| linux-release-x86_64 | OK | 185 | ||
| wasm-release | OK | 223 |
Exports:calc_dsgedsge_perm_testget_gaf_headerget_pathway_genesget_pathway_genes_dbget_pathway_genes_keggget_pathway_genes_reactomepathway_dsgeplot_dsgeplot_dsge_volcanoread_gafread_obo
Dependencies:data.tableevdPOTRcpp
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute DSGE (Disruption Score of Gene Expression) | calc_dsge |
| Permutation test for DSGE enrichment of a single gene set | dsge_perm_test |
| Extract header lines from a GAF file | get_gaf_header |
| Extract gene-pathway (GO term) associations from GAF data | get_pathway_genes |
| Build pathway-gene mapping from a Bioconductor OrgDb object | get_pathway_genes_db |
| Build KEGG pathway-gene mapping from a Bioconductor OrgDb object | get_pathway_genes_kegg |
| Build Reactome pathway-gene mapping from a Bioconductor OrgDb object | get_pathway_genes_reactome |
| Pathway-level DSGE permutation test with FDR correction | pathway_dsge |
| Plot null distribution vs. observed DSGE for selected pathways | plot_dsge |
| Gene-level volcano plot for a specific pathway | plot_dsge_volcano |
| Read a Gene Ontology Annotation File (GAF) | read_gaf |
| Read GO term names from an OBO file | read_obo |
