HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.
BACKGROUND
High-throughput screens (HTS) by RNAi or small molecules are among the most promising tools in functional genomics. They enable researchers to observe detailed reactions to experimental perturbations on a genome-wide scale. While there is a core set of computational approaches used in many publications to analyze these data, a specialized software combining them and making them easily accessible has so far been missing.


RESULTS
Here we describe HTSanalyzeR, a flexible software to build integrated analysis pipelines for HTS data that contains over-representation analysis, gene set enrichment analysis, comparative gene set analysis and rich sub-network identification. HTSanalyzeR interfaces with commonly used pre-processing packages for HTS data and presents its results as HTML pages and network plots.


BACKGROUND
Our software is written in the R language and freely available via the Bioconductor project at http://www.bioconductor.org.
Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK.
Xin
X
Wang
Camille
C
Terfve
John C
JC
Rose
Florian
F
Markowetz
D019295:Computational Biology / Q000379:methods*; D053263:Gene Regulatory Networks; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010641:Phenotype; D034622:RNA Interference; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software
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