Man pages for CityUHK-CompBio/HTSanalyzeR2
Gene set over-representation, enrichment and network analyses for high- throughput data and corresponding time-series data

analyzeGene Set Collection Analysis or NetWork Analysis
analyzeGscaTSGene Set Collection Analysis for Time-series data.
analyzeNwaTSSubnetwork analysis for Time-series data
annotationConvertorConvert between different types of gene identifiers
appendGSTermsAppend gene set terms to GSCA results
appendGSTermsTSAppend gene set terms to GSCA results for each GSCA object of...
Biogrid_HS_InteractomeAn object of class 'igraph'
Biogrid_HS_MatAn interactome matrix for _Homo Sapiens_
cellHTS2OutputStatTestsPerform statistical tests on a cellHTS object
d7CRISPR data set
d7_gscaAn object of class 'GSCA'
d7_nwaAn object of class 'NWA'
duplicateRemoverRemove duplicates in a named vector of phenotypes.
extractSubNet-NWA-methodExtract the subnetwork as an igraph object
getInteractomeAccessors for the 'interactome' slot of a 'NWA' object.
getParaAccessors for the 'para' slot of a 'GSCA' or 'fdr' slot of a...
getResultAccessors for the 'result' slot of a 'GSCA' or 'NWA' object.
getSummaryAccessors for the 'summary' slot of a 'GSCA' or 'NWA' object.
getTopGeneSetsSelect top significant gene sets from results of GSCA object
GOGeneSetsCreate a list of gene sets based on GO terms
GSCAAn S4 class for Gene Set Collection Analyses on...
GSCABatchAn S4 class for Time series data package in Gene Set...
gscaTSA list of 'GSCA' object
GSE33113_limmalimma result of a gene expression data
HTSanalyzeR2HTSanalyzeR2 Package Overview
HTSanalyzeR4MAGeCKAn analysis pipeline for CRISPR data preprocessed by MAGeCK
interactomeCreate an interactome from BioGRID database or input custom...
interactomeNwaTSCreate an interactome from BioGRID database or input custom...
KeggGeneSetsCreate a list of KEGG gene sets
MSigDBGeneSetsCreate a list of gene sets for Homo Sapiens based on MSigDB...
NWAAn S4 class for NetWork Analysis on high-throughput data
NWABatchAn S4 class for Time series data package in NetWork Analysis...
nwaTSA list of 'NWA' object
plotGSEAPlot and save figures of GSEA results for top significant...
preprocessA preprocessing method for objects of class GSCA or NWA
preprocessGscaTSA preprocessing method for a GSCABatch object of Time-series...
preprocessNwaTSA preprocessing method for a GSCABatch object of Time-series...
reportWrite HTML reports for enrichment or network analyses
reportAllWrite HTML reports for both enrichment and network analyses
summarizePrint summary information for an object of class GSCA or NWA
viewEnrichMap-GSCA-methodPlot the enrichment map for GSEA or GSOA result
viewGSEAPlot a figure of GSEA results for one gene set
viewSubNet-NWA-methodPlot the identified subnetwork of an NWA object
xnAn object of class 'cellHTS2'
CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 19, 2017, 4 p.m.