Package: RCPA 0.2.9

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. This package wraps functionality from 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 et al. (2012) <https://CRAN.R-project.org/package=CePa>.

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

RCPA_0.2.9.tar.gz
RCPA_0.2.9.zip(r-4.7-any)RCPA_0.2.9.zip(r-4.6-any)RCPA_0.2.9.zip(r-4.5-any)
RCPA_0.2.9.tgz(r-4.6-any)RCPA_0.2.9.tgz(r-4.5-any)
RCPA_0.2.9.tar.gz(r-4.7-any)RCPA_0.2.9.tar.gz(r-4.6-any)
RCPA_0.2.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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

On CRAN:

biobase deseq2 geoquery edger limma rcyjs fgsea browserviz summarizedexperiment annotationdbi rontotools

5.04 score 1 stars 73 scripts 338 downloads 28 exports 123 dependencies

Last updated from:f420349743. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	375
source / vignettes	OK	341
linux-release	OK	390
macos-release	OK	321
macos-oldrel	OK	374
windows-devel	OK	300
windows-release	OK	226
windows-oldrel	OK	241
wasm-release	OK	216

Exports:downloadGEO getCePaPathwayCatalogue getCommonDEGenes getCommonPathways getEntrezAnnotation getGeneSets getSPIAKEGGNetwork getSupportedPlatforms loadData plotBarChart plotDEGeneHeatmap plotForest plotKEGGMap plotMA plotPathwayHeatmap plotPathwayNetwork plotVennDE plotVennPathway plotVolcanoDE plotVolcanoPathway processAffymetrix processAgilent runConsensusAnalysis runDEAnalysis runDEMetaAnalysis runGeneSetAnalysis runPathwayAnalysis runPathwayMetaAnalysis

Dependencies:abind AnnotationDbi askpass base64enc BH Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocParallel Biostrings bit bit64 blob cachem class classInt cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DESeq2 digest dplyr e1071 edgeR farver fastmap filelock formatR futile.logger futile.options generics GenomicRanges GEOquery ggnewscale ggpattern ggplot2 ggrepel glue graph gridpattern gtable hms htmltools httr httr2 IRanges IRdisplay isoband jsonlite KEGGREST KernSmooth labeling lambda.r lattice lifecycle limma locfit magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress proxy purrr R.methodsS3 R.oo R.utils R6 RColorBrewer Rcpp RcppArmadillo readr rentrez repr rlang RobustRankAggreg RSQLite rvest s2 S4Arrays S4Vectors S7 scales selectr Seqinfo sf snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb units utf8 vctrs viridisLite vroom withr wk XML xml2 XVector

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

Rendered fromRCPA.Rmdusingknitr::knitr

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Download GEO data	downloadGEO
Get KEGG pathway catalogue (network) for CePa.ORA and CePa.GSA methods	getCePaPathwayCatalogue
Get common significant DE genes from multiple DE Analysis results	getCommonDEGenes
Retrieve common significant pathways from multiple pathway analysis results	getCommonPathways
Get Entrez annotation	getEntrezAnnotation
Get gene sets	getGeneSets
Get KEGG pathway network for SPIA method	getSPIAKEGGNetwork
Get supported platforms	getSupportedPlatforms
Load data from GitHub	loadData
Plot a bar chart of the pathway analysis results	plotBarChart
Plot gene heatmap from a SummarizedExperiment object with DE analysis results	plotDEGeneHeatmap
Plot pathway forest plot from pathway/geneset/meta analysis results	plotForest
Plot KEGG map with DE genes	plotKEGGMap
Plot MA plot from DE analysis results	plotMA
Plot pathways heatmap plot from pathway/geneset/meta analysis results	plotPathwayHeatmap
Plot a pathway network	plotPathwayNetwork
Plot Venn diagram from multiple DE Analysis results	plotVennDE
Plot Venn diagram from multiple pathway analysis results	plotVennPathway
Plot volcano plot from Pathway analysis results	plotVolcanoDE
Plot volcano plot from Pathway analysis results	plotVolcanoPathway
Process and normalize affymetrix-based dataset	processAffymetrix
Process and normalize agilent-based dataset	processAgilent
Perform Consensus Analysis	runConsensusAnalysis
Differential expression analysis	runDEAnalysis
Combine DE analysis results	runDEMetaAnalysis
Gene Set Enrichment Analysis	runGeneSetAnalysis
Topology-based Pathway Analysis	runPathwayAnalysis
Perform Meta Analysis	runPathwayMetaAnalysis