Package: RCPA 0.2.4

Ha Nguyen

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:Ha Nguyen [aut, cre], Phi Bya [aut], Zeynab Maghsoudi [aut], Tin Nguyen [fnd]

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'))

Peer review:

Bug tracker:https://github.com/tinnlab/rcpa/issues

On CRAN:

biobasedeseq2geoqueryedgerlimmarcyjsfgseabrowservizsummarizedexperimentannotationdbirontotools

5.79 score 1 stars 68 scripts 82 downloads 28 exports 129 dependencies

Last updated 2 days agofrom:beee33197e. Checks:OK: 6 WARNING: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 04 2024
R-4.5-winOKNov 04 2024
R-4.5-linuxWARNINGNov 04 2024
R-4.4-winOKNov 04 2024
R-4.4-macOKNov 04 2024
R-4.3-winOKNov 04 2024
R-4.3-macOKNov 04 2024

Exports:downloadGEOgetCePaPathwayCataloguegetCommonDEGenesgetCommonPathwaysgetEntrezAnnotationgetGeneSetsgetSPIAKEGGNetworkgetSupportedPlatformsloadDataplotBarChartplotDEGeneHeatmapplotForestplotKEGGMapplotMAplotPathwayHeatmapplotPathwayNetworkplotVennDEplotVennPathwayplotVolcanoDEplotVolcanoPathwayprocessAffymetrixprocessAgilentrunConsensusAnalysisrunDEAnalysisrunDEMetaAnalysisrunGeneSetAnalysisrunPathwayAnalysisrunPathwayMetaAnalysis

Dependencies:abindAnnotationDbiaskpassbase64encBHBiobaseBiocGenericsBiocManagerBiocParallelBiostringsbitbit64blobcachemclassclassIntclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDESeq2digestdplyre1071edgeRfansifarverfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGEOqueryggnewscaleggpatternggplot2ggrepelgluegraphgridpatterngtablehmshtmltoolshttrhttr2IRangesIRdisplayisobandjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrpngprettyunitsprogressproxypurrrR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloreadrrentrezreprrlangRobustRankAggregRSQLitervests2S4ArraysS4VectorsscalesselectrsfsnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsunitsutf8vctrsviridisLitevroomwithrwkXMLxml2XVectorzlibbioc

RCPA: an open-source R package for data processing, differential analysis, consensus pathway analysis, and visualization

Rendered fromRCPA.Rmdusingknitr::knitron Nov 04 2024.

Last update: 2023-11-28
Started: 2023-07-05

Readme and manuals

Help Manual

Help pageTopics
Download GEO datadownloadGEO
Get KEGG pathway catalogue (network) for CePa.ORA and CePa.GSA methodsgetCePaPathwayCatalogue
Get common significant DE genes from multiple DE Analysis resultsgetCommonDEGenes
Retrieve common significant pathways from multiple pathway analysis resultsgetCommonPathways
Get Entrez annotationgetEntrezAnnotation
Get gene setsgetGeneSets
Get KEGG pathway network for SPIA methodgetSPIAKEGGNetwork
Get supported platformsgetSupportedPlatforms
Load data from GitHubloadData
Plot a bar chart of the pathway analysis resultsplotBarChart
Plot gene heatmap from a SummarizedExperiment object with DE analysis resultsplotDEGeneHeatmap
Plot pathway forest plot from pathway/geneset/meta analysis resultsplotForest
Plot KEGG map with DE genesplotKEGGMap
Plot MA plot from DE analysis resultsplotMA
Plot pathways heatmap plot from pathway/geneset/meta analysis resultsplotPathwayHeatmap
Plot a pathway networkplotPathwayNetwork
Plot Venn diagram from multiple DE Analysis resultsplotVennDE
Plot Venn diagram from multiple pathway analysis resultsplotVennPathway
Plot volcano plot from Pathway analysis resultsplotVolcanoDE
Plot volcano plot from Pathway analysis resultsplotVolcanoPathway
Process and normalize affymetrix-based datasetprocessAffymetrix
Process and normalize agilent-based datasetprocessAgilent
Perform Consensus AnalysisrunConsensusAnalysis
Differential expression analysisrunDEAnalysis
Combine DE analysis resultsrunDEMetaAnalysis
Gene Set Enrichment AnalysisrunGeneSetAnalysis
Topology-based Pathway AnalysisrunPathwayAnalysis
Perform Meta AnalysisrunPathwayMetaAnalysis