Package: rgsepd 1.45.0
Karl Stamm
rgsepd: Gene Set Enrichment / Projection Displays
R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at transcript IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.
Authors:
rgsepd_1.45.0.tar.gz
rgsepd_1.45.0.zip(r-4.7)rgsepd_1.45.0.zip(r-4.6)rgsepd_1.45.0.zip(r-4.5)
rgsepd_1.45.0.tgz(r-4.6-any)rgsepd_1.45.0.tgz(r-4.5-any)
rgsepd_1.45.0.tar.gz(r-4.7-any)rgsepd_1.45.0.tar.gz(r-4.6-any)
rgsepd_1.45.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
rgsepd/json (API)
NEWS
| # Install 'rgsepd' in R: |
| install.packages('rgsepd', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- IlluminaBodymap - Sample RNA-Seq Counts data
- IlluminaBodymapMeta - Metadata table for the included sample data
On BioConductor:rgsepd-1.45.0(bioc 3.24)rgsepd-1.44.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologysoftwaredifferentialexpressiongenesetenrichmentrnaseq
Last updated from:a040b380d2. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 342 | ||
| linux-devel-x86_64 | NOTE | 578 | ||
| source / vignettes | OK | 561 | ||
| linux-release-x86_64 | NOTE | 701 | ||
| macos-release-arm64 | NOTE | 609 | ||
| macos-oldrel-arm64 | NOTE | 506 | ||
| windows-devel | NOTE | 681 | ||
| windows-release | NOTE | 591 | ||
| windows-oldrel | NOTE | 634 | ||
| wasm-release | OK | 234 |
Exports:DisplayNameExtractProjectionGSEPD_ChangeConditionsGSEPD_ChangeOutputGSEPD_DEGHeatmapGSEPD_Export_DESeqGSEPD_HeatmapGSEPD_INITGSEPD_PCA_PlotGSEPD_PCA_SpecGSEPD_ProcessGSEPD_ProcessAllGSEPD_PullDEGName_to_RefSeq
Dependencies:abindAnnotationDbiaskpassBHBiasedUrnBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcaToolscigarilloclicodetoolscpp11crayoncurlDBIdbplyrDelayedArrayDESeq2dplyrfarverfastmapfilelockformatRfutile.loggerfutile.optionsgeneLenDataBasegenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2glueGO.dbgoseqgplotsgtablegtoolshmshttrhttr2IRangesisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelocfitmagrittrMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslorg.Hs.eg.dbpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppRcppArmadilloRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttxdbmakerUCSC.utilsutf8vctrsviridisLitewithrXMLxml2XVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| R/Gene Set Enrichment and Projection Displays | rgsepd-package rgsepd |
| DisplayName | DisplayName |
| ExtractProjection | ExtractProjection |
| GSEPD_ChangeConditions | GSEPD_ChangeConditions |
| GSEPD_ChangeOutput | GSEPD_ChangeOutput |
| Differentially Expressed Genes Heatmap | GSEPD_DEGHeatmap |
| Export DESeqDataSet object | GSEPD_Export_DESeq |
| GSEPD_Heatmap | GSEPD_Heatmap |
| Initialization | GSEPD_INIT |
| Principle Components Analysis figure generation | GSEPD_PCA_Plot |
| Specialized PCA Plot | GSEPD_PCA_Spec |
| Processing | GSEPD_Process |
| GSEPD_ProcessAll | GSEPD_ProcessAll |
| Pull Differentially Expressed Genes | GSEPD_PullDEG |
| Sample RNA-Seq Counts data | IlluminaBodymap |
| Metadata table for the included sample data | IlluminaBodymapMeta |
| Name to RefSeq | Name_to_RefSeq |
