HTSanalyzeR: an R/Bioconductor Package for Integrated Network Analysis of High-throughput Screens

Overview

Journal Bioinformatics

Publisher Oxford University Press

Specialty Biology

Date 2011 Jan 25

PMID 21258062

Citations 80

Authors

Xin Wang

Camille Terfve

John C Rose

Florian Markowetz

Affiliations

Soon will be listed here.

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.

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