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These function can be used separately or sequentially\nto analyze RNA-Seq data.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "RoxygenNote": "7.1.2", "Config/testthat/edition": "3", "biocViews": "GeneExpression, GeneSetEnrichment, GeneTarget, miRNA,\nPathways", "URL": "https://github.com/pouryany/PanomiR", "BugReports": "https://github.com/pouryany/PanomiR/issues", "VignetteBuilder": "knitr", "Config/pak/sysreqs": "libcairo2-dev cmake libfftw3-dev libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:57:46 UTC", "RemoteUrl": "https://github.com/bioc/PanomiR", "RemoteRef": "HEAD", "RemoteSha": "d0a6310a04046e164845a0e7fdec6f72dfc3f2d1", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-30 07:23:50 UTC", "User": "root" }, "Author": "Pourya Naderi [aut, cre],\nYue Yang (Alan) Teo [aut],\nIlya Sytchev [aut],\nWinston Hide 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Each list item is a list of genes targeted by the respective miRNA family", "object": "targetScan_03", "file": "targetScan_03.rda", "class": [ "list" ], "fields": [], "table": false, "tojson": true } ], "_help": [ { "page": "alignToUniverse", "title": "function to align a list of sets and a reference universe", "topics": [ "alignToUniverse" ] }, { "page": "clusterPlot", "title": "Plots clusters of pathways with associated directionality.", "topics": [ "clusterPlot" ] }, { "page": "differentialPathwayAnalysis", "title": "Differential Expression Analysis For Pathways", "topics": [ "differentialPathwayAnalysis" ] }, { "page": "enrichAllPairs", "title": "Pairwise enrichment analysis between two given lists of sets", "topics": [ "enrichAllPairs" ] }, { "page": "getDesignMatrix", "title": "Obtain Design Matrix", "topics": [ "getDesignMatrix" ] }, { "page": "getDiffExpTable", "title": "function to get a DE table", "topics": [ "getDiffExpTable" ] }, { "page": "getResidual", "title": "function to get residuals with respect to a set of covariates", "topics": [ "getResidual" ] }, { "page": "gscExample", "title": "Example genesets from MSigDB", "topics": [ "gscExample" ] }, { "page": "jackKnifeBase", "title": "Outputs a table with col x (miRNA), probability of observing k (depending on methodology) against a random distribution with jack-knifing of the pathway cluster (removing a pathway at a time)", "topics": [ "jackKnifeBase" ] }, { "page": "linColumnFinder", "title": "Function imported from https://github.com/th1vairam/CovariateAnalysis Modified from http://stackoverflow.com/questions/13088770/ Function to find linearly dependednt columns of a matrix", "topics": [ "linColumnFinder" ] }, { "page": "mappingPathwaysClusters", "title": "Outputs a table with pathways and their respective clusters", "topics": [ "mappingPathwaysClusters" ] }, { "page": "methodProbBase", "title": "Outputs a table with col x, miRNA, probability of observing k against a random distribution of the cover of methodology", "topics": [ "methodProbBase" ] }, { "page": "miniTestsPanomiR", "title": "Readouts and datasets for minimal reproducible examples of the PanomiR.", "topics": [ "miniTestsPanomiR" ] }, { "page": "miRNAPathwayEnrichment", "title": "Enrichment Probability Of miRNAs", "topics": [ "miRNAPathwayEnrichment" ] }, { "page": "msigdb_c2", "title": "Canonical pathways from Molecular Signatures Database, MsigDb V6.2", "topics": [ "msigdb_c2" ] }, { "page": "path_gene_table", "title": "A table of gene-pathway association. based on the pathways of MSigDB.", "topics": [ "path_gene_table" ] }, { "page": "pathwayGeneTab", "title": "Pathway-Gene Associations", "topics": [ "pathwayGeneTab" ] }, { "page": "pathwaySummary", "title": "Pathway Summary Statistics", "topics": [ "pathwaySummary" ] }, { "page": "pcxnToNet", "title": "Creates a network out of pcxn table", "topics": [ "pcxnToNet" ] }, { "page": "prioritizeMicroRNA", "title": "Prioritize miRNA", "topics": [ "prioritizeMicroRNA" ] }, { "page": "reportEnrichment", "title": "Publication-ready miRNA-Pathway Enrichment table", "topics": [ "reportEnrichment" ] }, { "page": "samplingDataBase", "title": "Outputs a table of sampling data(rows are miRNA and cols are samples)", "topics": [ "samplingDataBase" ] }, { "page": "tableFromGSC", "title": "Pathway-Gene Associations from GeneSet collections", "topics": [ "tableFromGSC" ] }, { "page": "targetScan_03", "title": "A processed list of miRNA target gene sets from the TargetScan dataset. 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