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

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.