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 <firstname.lastname@example.org>, Camille Terfve <email@example.com>, John C. Rose <firstname.lastname@example.org>, Florian Markowetz <Florian.Markowetz@cruk.cam.ac.uk>|
|Date of publication||None|
|Maintainer||Xin Wang <email@example.com>|
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