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Bioinformatics. 2011 Mar 15;27(6):879-80. doi: 10.1093/bioinformatics/btr028. Epub 2011 Jan 22.

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

Author information

1
Cancer Research UK Cambridge Research Institute, Cambridge CB2 0RE, UK.

Abstract

MOTIVATION:

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.

AVAILABILITY:

Our software is written in the R language and freely available via the Bioconductor project at http://www.bioconductor.org.

PMID:
21258062
PMCID:
PMC3051329
DOI:
10.1093/bioinformatics/btr028
[Indexed for MEDLINE]
Free PMC Article

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