Package: pairedGSEA 1.12.0

Søren Helweg Dam

pairedGSEA: Paired DGE and DGS analysis for gene set enrichment analysis

pairedGSEA makes it simple to run a paired Differential Gene Expression (DGE) and Differencital Gene Splicing (DGS) analysis. The package allows you to store intermediate results for further investiation, if desired. pairedGSEA comes with a wrapper function for running an Over-Representation Analysis (ORA) and functionalities for plotting the results.

Authors:Søren Helweg Dam [cre, aut], Lars Rønn Olsen [aut], Kristoffer Vitting-Seerup [aut]

pairedGSEA_1.12.0.tar.gz
pairedGSEA_1.12.0.zip(r-4.7)pairedGSEA_1.12.0.zip(r-4.6)pairedGSEA_1.12.0.zip(r-4.5)
pairedGSEA_1.12.0.tgz(r-4.6-any)pairedGSEA_1.12.0.tgz(r-4.5-any)
pairedGSEA_1.12.0.tar.gz(r-4.7-any)pairedGSEA_1.12.0.tar.gz(r-4.6-any)
pairedGSEA_1.12.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
pairedGSEA/json (API)
NEWS

# Install 'pairedGSEA' in R:

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

Bug tracker:https://github.com/shdam/pairedgsea/issues

Datasets:

example_diff_result - Output of running paired_diff on example_se.
example_gene_sets - MSigDB gene sets from humans, category C5 with ensemble gene IDs
example_ora_results - Output of running paired_ora on example_diff_result and gene sets extracted from MSigDB
example_se - A small subset of the GEO:GSE61220 data set.

On BioConductor:pairedGSEA-1.13.0(bioc 3.24)pairedGSEA-1.12.0(bioc 3.23)

differentialexpression alternativesplicing differentialsplicing geneexpression immunooncology genesetenrichment pathways rnaseq software transcription

4.60 score 4 stars 1 scripts 262 downloads 4 exports 115 dependencies

Last updated from:79ba22dab9 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

Target	Result	Time
bioc-checks	NOTE	210
linux-devel-x86_64	OK	513
source / vignettes	OK	387
linux-release-x86_64	OK	492
macos-release-arm64	OK	339
macos-oldrel-arm64	OK	306
windows-devel	OK	450
windows-release	OK	384
windows-oldrel	OK	437
wasm-release	OK	162

Exports:paired_diff paired_ora plot_ora prepare_msigdb

Dependencies:abind aggregation annotate AnnotationDbi askpass assertthat babelgene BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem cli codetools cowplot cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 DEXSeq dplyr edgeR farver fastmap fastmatch fgsea filelock formatR futile.logger futile.options genefilter geneplotter generics GenomicRanges ggplot2 glue gtable hms httr httr2 hwriter IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mgcv mime msigdbr nlme openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo Rhtslib rlang Rsamtools RSQLite S4Arrays S4Vectors S7 scales Seqinfo showtext showtextdb snow SparseArray statmod stringi stringr SummarizedExperiment survival sva sys sysfonts tibble tidyr tidyselect utf8 vctrs viridisLite withr XML xml2 xtable XVector

User Guide

Søren Helweg Dam

Rendered fromUser-Guide.Rmdusingknitr::rmarkdownon May 28 2026.

Last update: 2025-03-31
Started: 2022-08-09

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Output of running paired_diff on example_se.	example_diff_result
MSigDB gene sets from humans, category C5 with ensemble gene IDs	example_gene_sets
Output of running paired_ora on example_diff_result and gene sets extracted from MSigDB	example_ora_results
A small subset of the GEO:GSE61220 data set.	example_se
Run paired DESeq2 and DEXSeq analyses	paired_diff
Paired Over-Representation Analysis	paired_ora
Scatter plot of Over-Representation Analysis results	plot_ora
Load MSigDB and convert to names list of gene sets	prepare_msigdb