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


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Documentation for package ‘HTSanalyzeR’ version 2.36.0

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HTSanalyzeR-package HTSanalyzeR Package Overview
aggregatePvals Aggregate p-values from gene set over-representation tests.
analyze Gene Set Collection Analysis or NetWork Analysis
analyze-method Gene Set Collection Analysis or NetWork Analysis
analyzeGeneSetCollections Hypergeometric tests and Gene Set Enrichment Analyses over a list of gene set collections
annotationConvertor Convert between different types of gene identifiers
appendGSTerms Append gene set terms to GSCA results
appendGSTerms-method Append gene set terms to GSCA results
biogridDataDownload Download and extract a network interaction matrix from a BioGRID data set
Biogrid_DM_Interactome A Sample data set of the package HTSanalyzeR
Biogrid_DM_Mat A Sample data set of the package HTSanalyzeR
celAnnotationConvertor Convert between different types of gene identifiers for Caenorhabditis Elegans
cellHTS2OutputStatTests Perform statistical tests on a cellHTS object
changes View new changes made in the latest version
collectionGsea Compute observed and permutation-based enrichment scores for a collection (list) of gene sets
drosoAnnotationConvertor Convert between different types of gene identifiers for Drosophila Melanogaster
duplicateRemover Remove duplicates in a named vector of phenotypes
FDRcollectionGsea Compute the GSEA false discovery rates for a collection (list) of gene sets
getTopGeneSets Select top significant gene sets from GSEA results
getTopGeneSets-method Select top significant gene sets from GSEA results
GOGeneSets Create a list of gene sets based on GO terms
GSCA An S4 class for Gene Set Collection Analyses on high-throughput screens
GSCA-class An S4 class for Gene Set Collection Analyses on high-throughput screens
gseaPlots Plot GSEA results for one gene set
gseaScores Compute enrichment scores for GSEA (Gene Set Enrichment Analysis)
gseaScoresBatch Compute enrichment scores for GSEA (Gene Set Enrichment Analysis)
gseaScoresBatchParallel Compute enrichment scores for GSEA (Gene Set Enrichment Analysis)
HTSanalyzeR HTSanalyzeR Package Overview
HTSanalyzeR4cellHTS2 An analysis pipeline for cellHTS2 objects
hyperGeoTest Performs hypergeometric tests for over-representation analysis
interactome Create an interactome from BioGRID data sets
interactome-method Create an interactome from BioGRID data sets
KcViab_Data4Enrich A Sample data set of the package HTSanalyzeR
KcViab_GSCA A Sample data set of the package HTSanalyzeR
KcViab_Norm A Sample data set of the package HTSanalyzeR
KcViab_NWA A Sample data set of the package HTSanalyzeR
KcViab_PVals A Sample data set of the package HTSanalyzeR
KeggGeneSets Create a list of gene sets based on KEGG pathways terms
mammalAnnotationConvertor Convert between different types of identifiers for mammalian species
multiHyperGeoTest Hypergeometric tests on a list of gene sets
networkAnalysis Identify enriched subnetworks
networkPlot Plot the enriched subnetwork
NWA An S4 class for NetWork Analysis on high-throughput screens
NWA-class An S4 class for NetWork Analysis on high-throughput screens
pairwiseGsea GSEA on a pair of phenotypes
pairwiseGseaPlot Produce a plot for pairwise GSEA result on one gene set
pairwisePhenoMannWhit Mann-Whitney U test for shift in location of genes from gene sets on a pair of phenotypes
permutationPvalueCollectionGsea Compute the GSEA p-values for a list of gene sets
plotEnrichMap Plot and save an enrichment map for results of GSEA or hypergeometric tests
plotEnrichMap-method Plot and save an enrichment map for results of GSEA or hypergeometric tests
plotGSEA Plot and save figures of GSEA results for top significant gene sets
plotGSEA-method Plot and save figures of GSEA results for top significant gene sets
plotSubNet Plot and save a figure of the enriched subnetwork
plotSubNet-method Plot and save a figure of the enriched subnetwork
preprocess A preprocessing method for objects of class GSCA or NWA
preprocess-method A preprocessing method for objects of class GSCA or NWA
report Write HTML reports for enrichment or network analyses
report-method Write HTML reports for enrichment or network analyses
reportAll Write HTML reports for both the enrichment and network analyses
reportAll-method Write HTML reports for both the enrichment and network analyses
show Print summary information for an object of class GSCA or NWA
show-method Print summary information for an object of class GSCA or NWA
summarize Print summary information for an object of class GSCA or NWA
summarize-method Print summary information for an object of class GSCA or NWA
viewEnrichMap Plot a figure of the enrichment map for GSEA or Hypergeometric tests
viewEnrichMap-method Plot a figure of the enrichment map for GSEA or Hypergeometric tests
viewGSEA Plot a figure of GSEA results for one gene set
viewGSEA-method Plot a figure of GSEA results for one gene set
viewSubNet Plot a figure of the enriched subnetwork
viewSubNet-method Plot a figure of the enriched subnetwork
writeHits An S4 class for Gene Set Collection Analyses on high-throughput screens
writeHits-method An S4 class for Gene Set Collection Analyses on high-throughput screens
writeReportHTSA Write HTML reports for enrichment and/or network analyses