HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens
Version 2.28.0

This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over-representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.

Browse man pages Browse package API and functions Browse package files

AuthorXin Wang <xinwang2hms@gmail.com>, Camille Terfve <cdat2@cam.ac.uk>, John C. Rose <jcr53@cam.ac.uk>, Florian Markowetz <Florian.Markowetz@cruk.cam.ac.uk>
Bioconductor views CellBasedAssays MultipleComparison
Date of publicationNone
MaintainerXin Wang <xinwang2hms@gmail.com>
LicenseArtistic-2.0
Version2.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HTSanalyzeR")

Man pages

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...
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...
celAnnotationConvertor: Convert between different types of gene identifiers for...
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...
data-KcViab: A Sample data set of the package HTSanalyzeR
drosoAnnotationConvertor: Convert between different types of gene identifiers for...
duplicateRemover: Remove duplicates in a named vector of phenotypes
FDRcollectionGsea: Compute the GSEA false discovery rates for a collection...
GenHTSAHtmlRowUnit: Generate html codes for one unit of a row of a table
getTopGeneSets: Select top significant gene sets from GSEA results
GOGeneSets: Create a list of gene sets based on GO terms
GSCA-class: An S4 class for Gene Set Collection Analyses on...
gseaPlots: Plot GSEA results for one gene set
gseaScores: Compute enrichment scores for GSEA (Gene Set Enrichment...
htmlAttrVectorPaste: Collapse an attribute vector for a table unit
HTSanalyzeR: HTSanalyzeR Package Overview
HTSanalyzeR4cellHTS2: An analysis pipeline for cellHTS2 objects
hyperGeoTest: Performs hypergeometric tests for over-representation...
interactome: Create an interactome from BioGRID data sets
KeggGeneSets: Create a list of gene sets based on KEGG pathways terms
makeGSEAplots: Produce GSEA plots
makeOverlapTable: Find and save the overlapped genes between a gene set and a...
mammalAnnotationConvertor: Convert between different types of identifiers for mammalian...
multiHyperGeoTest: Hypergeometric tests on a list of gene sets
networkAnalysis: Identify enriched subnetworks
networkPlot: Plot the enriched subnetwork
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...
paraCheck: Check parameters
permutationPvalueCollectionGsea: Compute the GSEA p-values for a list of gene sets
plotEnrichMap: Plot and save an enrichment map for results of GSEA or...
plotGSEA: Plot and save figures of GSEA results for top significant...
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...
summarize: Print summary information for an object of class GSCA or NWA
viewEnrichMap: Plot a figure of the enrichment map for GSEA or...
viewGSEA: Plot a figure of GSEA results for one gene set
viewSubNet: Plot a figure of the enriched subnetwork
writeHTSAHtmlHead: Write the head part of report htmls
writeHTSAHtmlSummary: Write the summary part of report htmls
writeHTSAHtmlTab: Write tabs to report htmls
writeHTSAHtmlTable: Write a table to report htmls
writeHTSAHtmlTail: Write the tail part of report htmls
writeReportHTSA: Write HTML reports for enrichment and/or network analyses

Functions

Biogrid_DM_Interactome Man page
Biogrid_DM_Mat Man page
FDRcollectionGsea Man page Source code
GOGeneSets Man page Source code
GSCA Man page
GSCA-class Man page
GenHTSAHtmlRowUnit Man page Source code
HTSanalyzeR Man page
HTSanalyzeR-package Man page
HTSanalyzeR4cellHTS2 Man page Source code
KcViab_Data4Enrich Man page
KcViab_GSCA Man page
KcViab_NWA Man page
KcViab_Norm Man page
KcViab_PVals Man page
KeggGeneSets Man page Source code
NWA Man page
NWA-class Man page
aggregatePvals Man page Source code
analyze Man page
analyze,GSCA-method Man page
analyze,NWA-method Man page
analyzeGeneSetCollections Man page Source code
annotationConvertor Man page Source code
appendGSTerms Man page
appendGSTerms,GSCA-method Man page
biogridDataDownload Man page Source code
celAnnotationConvertor Man page Source code
cellHTS2OutputStatTests Man page Source code
changes Man page Source code
collectionGsea Man page Source code
drosoAnnotationConvertor Man page Source code
duplicateRemover Man page Source code
getTopGeneSets Man page
getTopGeneSets,GSCA-method Man page
gseaPlots Man page Source code
gseaScores Man page Source code
gseaScoresBatch Man page Source code
gseaScoresBatchParallel Man page Source code
htmlAttrVectorPaste Man page Source code
hyperGeoTest Man page Source code
interactome Man page
interactome,NWA-method Man page
makeGSEAplots Man page Source code
makeOverlapTable Man page Source code
mammalAnnotationConvertor Man page Source code
multiHyperGeoTest Man page Source code
networkAnalysis Man page Source code
networkPlot Man page Source code
onLoad Source code
pairwiseGsea Man page Source code
pairwiseGseaPlot Man page Source code
pairwisePhenoMannWhit Man page Source code
paraCheck Man page Source code
permutationPvalueCollectionGsea Man page Source code
plotEnrichMap Man page
plotEnrichMap,GSCA-method Man page
plotGSEA Man page
plotGSEA,GSCA-method Man page
plotSubNet Man page
plotSubNet,NWA-method Man page
preprocess Man page
preprocess,GSCA-method Man page
preprocess,NWA-method Man page
report Man page
report,GSCA-method Man page
report,NWA-method Man page
reportAll Man page
reportAll,GSCA_Or_NULL,NWA_Or_NULL-method Man page
show Man page
show,GSCA-method Man page
show,NWA-method Man page
summarize Man page
summarize,GSCA-method Man page
summarize,NWA-method Man page
viewEnrichMap Man page
viewEnrichMap,GSCA-method Man page
viewGSEA Man page
viewGSEA,GSCA-method Man page
viewSubNet Man page
viewSubNet,NWA-method Man page
writeHTSAHtmlHead Man page Source code
writeHTSAHtmlSummary Man page Source code
writeHTSAHtmlTab Man page Source code
writeHTSAHtmlTable Man page Source code
writeHTSAHtmlTail Man page Source code
writeHits Man page
writeHits,GSCA-method Man page
writeReportHTSA Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R
R/AllGenerics.R
R/FDRcollectionGsea.R
R/GOGeneSets.R
R/GSCA-methods.R
R/HTSanalyzeR-internal.R
R/HTSanalyzeR4cellHTS2.R
R/KeggGeneSets.R
R/NWA-methods.R
R/aggregatePvals.R
R/analyzeGeneSetCollections.R
R/annotationConvertor.R
R/biogridDataDownload.R
R/celAnnotationConvertor.R
R/cellHTS2OutputStatTests.R
R/classUnions.R
R/collectionGsea.R
R/drosoAnnotationConvertor.R
R/duplicateRemover.R
R/gseaPlots.R
R/gseaScores.R
R/gseaScoresBatch.R
R/gseaScoresBatchParallel.R
R/hyperGeoTest.R
R/mammalAnnotationConvertor.R
R/multiHyperGeoTest.R
R/networkAnalysis.R
R/networkPlot.R
R/pairwiseGsea.R
R/pairwiseGseaPlot.R
R/pairwisePhenoMannWhit.R
R/paraCheck.R
R/permutationPvalueCollectionGsea.R
R/writeHtml.R
R/writeReportHTSA.R
R/zzz.R
build
build/vignette.rds
data
data/Biogrid_DM_Interactome.RData
data/Biogrid_DM_Mat.RData
data/KcViab_Data4Enrich.RData
data/KcViab_GSCA.RData
data/KcViab_NWA.RData
data/KcViab_Norm.RData
data/KcViab_PVals.RData
data/datalist
inst
inst/CHANGES
inst/CITATION
inst/doc
inst/doc/HTSanalyzeR-Vignette.R
inst/doc/HTSanalyzeR-Vignette.Rnw
inst/doc/HTSanalyzeR-Vignette.pdf
inst/templates
inst/templates/Rlogo.png
inst/templates/blue_cruklogo.gif
inst/templates/bordercorner.gif
inst/templates/goatcomputer.png
inst/templates/htsanalyzer.css
man
man/FDRcollectionGsea.Rd
man/GOGeneSets.Rd
man/GSCA-class.Rd
man/GenHTSAHtmlRowUnit.Rd
man/HTSanalyzeR.Rd
man/HTSanalyzeR4cellHTS2.Rd
man/KeggGeneSets.Rd
man/NWA-class.Rd
man/aggregatePvals.Rd
man/analyze.Rd
man/analyzeGeneSetCollections.Rd
man/annotationConvertor.Rd
man/appendGSTerms.Rd
man/biogridDataDownload.Rd
man/celAnnotationConvertor.Rd
man/cellHTS2OutputStatTests.Rd
man/changes.Rd
man/collectionGsea.Rd
man/data-KcViab.Rd
man/drosoAnnotationConvertor.Rd
man/duplicateRemover.Rd
man/getTopGeneSets.Rd
man/gseaPlots.Rd
man/gseaScores.Rd
man/htmlAttrVectorPaste.Rd
man/hyperGeoTest.Rd
man/interactome.Rd
man/makeGSEAplots.Rd
man/makeOverlapTable.Rd
man/mammalAnnotationConvertor.Rd
man/multiHyperGeoTest.Rd
man/networkAnalysis.Rd
man/networkPlot.Rd
man/pairwiseGsea.Rd
man/pairwiseGseaPlot.Rd
man/pairwisePhenoMannWhit.Rd
man/paraCheck.Rd
man/permutationPvalueCollectionGsea.Rd
man/plotEnrichMap.Rd
man/plotGSEA.Rd
man/plotSubNet.Rd
man/preprocess.Rd
man/report.Rd
man/reportAll.Rd
man/summarize.Rd
man/viewEnrichMap.Rd
man/viewGSEA.Rd
man/viewSubNet.Rd
man/writeHTSAHtmlHead.Rd
man/writeHTSAHtmlSummary.Rd
man/writeHTSAHtmlTab.Rd
man/writeHTSAHtmlTable.Rd
man/writeHTSAHtmlTail.Rd
man/writeReportHTSA.Rd
vignettes
vignettes/Figure.pdf
vignettes/HTSanalyzeR-Vignette.Rnw
HTSanalyzeR documentation built on May 20, 2017, 10:38 p.m.