HTSanalyzeR

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

Bioconductor version: 2.8

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 <Xin.Wang at cancer.org.uk>, Camille Terfve <cdat2 at cam.ac.uk>, John C. Rose <jcr53 at cam.ac.uk>, Florian Markowetz <Florian.Markowetz at cancer.org.uk>

Maintainer: Xin Wang <Xin.Wang at cancer.org.uk>

To install this package, start R and enter:

    source("http://bioconductor.org/biocLite.R")
    biocLite("HTSanalyzeR")

To cite this package in a publication, start R and enter:

    citation("HTSanalyzeR")

Documentation

PDF Figure.pdf
PDF R Script Main vignette:Gene set enrichment and network analysis of high-throughput RNAi screen data using HTSanalyzeR
PDF   Reference Manual

Details

biocViews CellBasedAssays, Bioinformatics, MultipleComparisons
Depends igraph, GSEABase, BioNet, cellHTS2, RankProd, methods
Imports graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt
Suggests KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow
System Requirements
License Artistic-2.0
URL
Depends On Me
Imports Me
Suggests Me
Version 2.5.1
Since Bioconductor 2.7 (R-2.12)

Package Downloads

Package Source HTSanalyzeR_2.5.1.tar.gz
Windows Binary HTSanalyzeR_2.5.1.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary HTSanalyzeR_2.5.1.tgz
Package Downloads Report Download Stats

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