HTSanalyzeR

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

Bioconductor version: Development (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, Camille Terfve , John C. Rose, Florian Markowetz

Maintainer: Xin Wang

To install this package, start R and enter:

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

Documentation

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

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	2.3.5

Package Downloads

Package Source	HTSanalyzeR_2.3.5.tar.gz
Windows Binary	HTSanalyzeR_2.3.5.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary	HTSanalyzeR_2.3.5.tgz
Package Downloads Report	Download Stats