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

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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.

Author
Xin 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>
Date of publication
None
Maintainer
Xin Wang <xinwang2hms@gmail.com>
License
Artistic-2.0
Version
2.26.0

View on Bioconductor

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

Files in this package

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