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

## Documentation for package ‘HTSanalyzeR’ version 2.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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