Man pages for HTSanalyzeR
Gene set over-representation, enrichment and network analyses for high-throughput screens

aggregatePvalsAggregate p-values from gene set over-representation tests.
analyzeGene Set Collection Analysis or NetWork Analysis
analyzeGeneSetCollectionsHypergeometric tests and Gene Set Enrichment Analyses over a...
annotationConvertorConvert between different types of gene identifiers
appendGSTermsAppend gene set terms to GSCA results
biogridDataDownloadDownload and extract a network interaction matrix from a...
celAnnotationConvertorConvert between different types of gene identifiers for...
cellHTS2OutputStatTestsPerform statistical tests on a cellHTS object
changesView new changes made in the latest version
collectionGseaCompute observed and permutation-based enrichment scores for...
data-KcViabA Sample data set of the package HTSanalyzeR
drosoAnnotationConvertorConvert between different types of gene identifiers for...
duplicateRemoverRemove duplicates in a named vector of phenotypes
FDRcollectionGseaCompute the GSEA false discovery rates for a collection...
GenHTSAHtmlRowUnitGenerate html codes for one unit of a row of a table
getTopGeneSetsSelect top significant gene sets from GSEA results
GOGeneSetsCreate a list of gene sets based on GO terms
GSCA-classAn S4 class for Gene Set Collection Analyses on...
gseaPlotsPlot GSEA results for one gene set
gseaScoresCompute enrichment scores for GSEA (Gene Set Enrichment...
htmlAttrVectorPasteCollapse an attribute vector for a table unit
HTSanalyzeRHTSanalyzeR Package Overview
HTSanalyzeR4cellHTS2An analysis pipeline for cellHTS2 objects
hyperGeoTestPerforms hypergeometric tests for over-representation...
interactomeCreate an interactome from BioGRID data sets
KeggGeneSetsCreate a list of gene sets based on KEGG pathways terms
makeGSEAplotsProduce GSEA plots
makeOverlapTableFind and save the overlapped genes between a gene set and a...
mammalAnnotationConvertorConvert between different types of identifiers for mammalian...
multiHyperGeoTestHypergeometric tests on a list of gene sets
networkAnalysisIdentify enriched subnetworks
networkPlotPlot the enriched subnetwork
NWA-classAn S4 class for NetWork Analysis on high-throughput screens
pairwiseGseaGSEA on a pair of phenotypes
pairwiseGseaPlotProduce a plot for pairwise GSEA result on one gene set
pairwisePhenoMannWhitMann-Whitney U test for shift in location of genes from gene...
paraCheckCheck parameters
permutationPvalueCollectionGseaCompute the GSEA p-values for a list of gene sets
plotEnrichMapPlot and save an enrichment map for results of GSEA or...
plotGSEAPlot and save figures of GSEA results for top significant...
plotSubNetPlot and save a figure of the enriched subnetwork
preprocessA preprocessing method for objects of class GSCA or NWA
reportWrite HTML reports for enrichment or network analyses
reportAllWrite HTML reports for both the enrichment and network...
summarizePrint summary information for an object of class GSCA or NWA
viewEnrichMapPlot a figure of the enrichment map for GSEA or...
viewGSEAPlot a figure of GSEA results for one gene set
viewSubNetPlot a figure of the enriched subnetwork
writeHTSAHtmlHeadWrite the head part of report htmls
writeHTSAHtmlSummaryWrite the summary part of report htmls
writeHTSAHtmlTabWrite tabs to report htmls
writeHTSAHtmlTableWrite a table to report htmls
writeHTSAHtmlTailWrite the tail part of report htmls
writeReportHTSAWrite HTML reports for enrichment and/or network analyses
HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.