Package: pairedGSEA 1.7.0
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:
pairedGSEA_1.7.0.tar.gz
pairedGSEA_1.7.0.zip(r-4.5)pairedGSEA_1.7.0.zip(r-4.4)pairedGSEA_1.7.0.zip(r-4.3)
pairedGSEA_1.7.0.tgz(r-4.5-any)pairedGSEA_1.7.0.tgz(r-4.4-any)pairedGSEA_1.7.0.tgz(r-4.3-any)
pairedGSEA_1.7.0.tar.gz(r-4.5-noble)pairedGSEA_1.7.0.tar.gz(r-4.4-noble)
pairedGSEA_1.7.0.tgz(r-4.4-emscripten)pairedGSEA_1.7.0.tgz(r-4.3-emscripten)
pairedGSEA.pdf |pairedGSEA.html✨
pairedGSEA/json (API)
NEWS
| # Install 'pairedGSEA' in R: |
| install.packages('pairedGSEA', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/shdam/pairedgsea/issues
- 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-1.7.0(bioc 3.21)pairedGSEA-1.6.0(bioc 3.20)
differentialexpressionalternativesplicingdifferentialsplicinggeneexpressionimmunooncologygenesetenrichmentpathwaysrnaseqsoftwaretranscription
Last updated 8 days agofrom:7731ffec81. Checks:7 OK, 1 WARNING. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 13 2025 |
| R-4.5-win | OK | Feb 13 2025 |
| R-4.5-mac | WARNING | Feb 13 2025 |
| R-4.5-linux | OK | Feb 13 2025 |
| R-4.4-win | OK | Feb 13 2025 |
| R-4.4-mac | OK | Feb 13 2025 |
| R-4.3-win | OK | Feb 13 2025 |
| R-4.3-mac | OK | Feb 13 2025 |
Exports:paired_diffpaired_oraplot_oraprepare_msigdb
Dependencies:abindaggregationannotateAnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDESeq2DEXSeqdigestdplyredgeRfansifarverfastmapfastmatchfgseafilelockformatRfutile.loggerfutile.optionsgenefiltergeneplottergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehmshttrhttr2hwriterIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRhtslibrlangRsamtoolsRSQLiteS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLxml2xtableXVector
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 |
