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

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.

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>
Date of publicationNone
MaintainerXin Wang <xinwang2hms@gmail.com>
LicenseArtistic-2.0
Version2.26.0

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

Functions

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

Files

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

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