HTSanalyzeR: An R/Bioconductor Package for Integrated Network Analysis of High-Throughput Screens

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

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology / methods*
  • Gene Regulatory Networks
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Phenotype
  • RNA Interference
  • Sequence Analysis, DNA / methods
  • Software*