HTSanalyzeR

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

Bioconductor version: Development (3.0)

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 <xinwang2hms at gmail.com>, Camille Terfve <cdat2 at cam.ac.uk>, John C. Rose <jcr53 at cam.ac.uk>, Florian Markowetz <Florian.Markowetz at cruk.cam.ac.uk>

Maintainer: Xin Wang <xinwang2hms at gmail.com>

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

Details

biocViews CellBasedAssays, MultipleComparison, Software
Version 2.17.0
In Bioconductor since BioC 2.7 (R-2.12)
License Artistic-2.0
Depends R (>= 2.15), igraph, methods
Imports graph, igraph, GSEABase, BioNet, cellHTS2, AnnotationDbi, biomaRt, RankProd
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
URL
Depends On Me
Imports Me Mulder2012, phenoTest
Suggests Me RTN

Package Downloads

Package Source HTSanalyzeR_2.17.0.tar.gz
Windows Binary HTSanalyzeR_2.17.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) HTSanalyzeR_2.17.0.tgz
Mac OS X 10.9 (Mavericks)
Package Downloads Report Download Stats

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