FDRcollectionGsea       Compute the GSEA false discovery rates for a
                        collection (list) of gene sets
GOGeneSets              Create a list of gene sets based on GO terms
GSCA-class              An S4 class for Gene Set Collection Analyses on
                        high-throughput screens
HTSanalyzeR-package     HTSanalyzeR Package Overview
HTSanalyzeR4cellHTS2    An analysis pipeline for cellHTS2 objects
KcViab_Norm             A Sample data set of the package HTSanalyzeR
KeggGeneSets            Create a list of gene sets based on KEGG
                        pathways terms
NWA-class               An S4 class for NetWork Analysis on
                        high-throughput screens
aggregatePvals          Aggregate p-values from gene set
                        over-representation tests.
analyze                 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
biogridDataDownload     Download and extract a network interaction
                        matrix from a BioGRID data set
celAnnotationConvertor
                        Convert between different types of gene
                        identifiers for Caenorhabditis Elegans
cellHTS2OutputStatTests
                        Perform statistical tests on a cellHTS object
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
getTopGeneSets          Select top significant gene sets from GSEA
                        results
gseaPlots               Plot GSEA results for one gene set
gseaScores              Compute enrichment scores for GSEA (Gene Set
                        Enrichment Analysis)
hyperGeoTest            Performs hypergeometric tests for
                        over-representation analysis
interactome             Create an interactome from BioGRID data sets
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
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
plotGSEA                Plot and save figures of GSEA results for top
                        significant gene sets
plotSubNet              Plot and save a figure of the enriched
                        subnetwork
preprocess              A preprocessing method for objects of class
                        GSCA or NWA
report                  Write HTML reports for enrichment or network
                        analyses
reportAll               Write HTML reports for both the enrichment and
                        network analyses
summarize               Print summary information for an object of
                        class GSCA or NWA
viewEnrichMap           Plot a figure of the enrichment map for GSEA or
                        Hypergeometric tests
viewGSEA                Plot a figure of GSEA results for one gene set
viewSubNet              Plot a figure of the enriched subnetwork
writeReportHTSA         Write HTML reports for enrichment and/or
                        network analyses
