Package: RCPA 0.2.4
RCPA: Consensus Pathway Analysis
Provides a set of functions to perform pathway analysis and meta analysis from multiple gene expression datasets, as well as visualization of the results (Nguyen et al. (2024). The package is a wrapper of the following packages: Ritchie et al. (2015) <doi:10.1093/nar/gkv007>, Love et al. (2014) <doi:10.1186/s13059-014-0550-8>, Robinson et al. (2010) <doi:10.1093/bioinformatics/btp616>, Korotkevich et al. (2016) <arxiv:10.1101/060012>, Efron et al. (2015) <https://CRAN.R-project.org/package=GSA>, and Gu, Z. (2012) <https://CRAN.R-project.org/package=CePa>.
Authors:
RCPA_0.2.4.tar.gz
RCPA_0.2.4.zip(r-4.5)RCPA_0.2.4.zip(r-4.4)RCPA_0.2.4.zip(r-4.3)
RCPA_0.2.4.tgz(r-4.4-any)RCPA_0.2.4.tgz(r-4.3-any)
RCPA_0.2.4.tar.gz(r-4.5-noble)RCPA_0.2.4.tar.gz(r-4.4-noble)
RCPA_0.2.4.tgz(r-4.4-emscripten)RCPA_0.2.4.tgz(r-4.3-emscripten)
RCPA.pdf |RCPA.html✨
RCPA/json (API)
# Install 'RCPA' in R: |
install.packages('RCPA', repos = c('https://tinnlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tinnlab/rcpa/issues
biobasedeseq2geoqueryedgerlimmarcyjsfgseabrowservizsummarizedexperimentannotationdbirontotools
Last updated 2 days agofrom:beee33197e. Checks:OK: 6 WARNING: 1. Indexed: yes.
Target | Result | Date |
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Doc / Vignettes | OK | Nov 04 2024 |
R-4.5-win | OK | Nov 04 2024 |
R-4.5-linux | WARNING | Nov 04 2024 |
R-4.4-win | OK | Nov 04 2024 |
R-4.4-mac | OK | Nov 04 2024 |
R-4.3-win | OK | Nov 04 2024 |
R-4.3-mac | OK | Nov 04 2024 |
Exports:downloadGEOgetCePaPathwayCataloguegetCommonDEGenesgetCommonPathwaysgetEntrezAnnotationgetGeneSetsgetSPIAKEGGNetworkgetSupportedPlatformsloadDataplotBarChartplotDEGeneHeatmapplotForestplotKEGGMapplotMAplotPathwayHeatmapplotPathwayNetworkplotVennDEplotVennPathwayplotVolcanoDEplotVolcanoPathwayprocessAffymetrixprocessAgilentrunConsensusAnalysisrunDEAnalysisrunDEMetaAnalysisrunGeneSetAnalysisrunPathwayAnalysisrunPathwayMetaAnalysis
Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiostringsbitbit64blobcachemclassclassIntclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDESeq2digestdplyre1071edgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOqueryggnewscaleggpatternggplot2ggrepelgluegraphgridpatterngtablehmshtmltoolshttrhttr2IRangesIRdisplayisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogressproxypurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrrentrezreprrlangRobustRankAggregRSQLitervests2S4ArraysS4VectorsscalesselectrsfsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsunitsutf8vctrsviridisLitevroomwithrwkXMLxml2XVectorzlibbioc