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Oxford University Press (OUP), Bioinformatics, 6(27), p. 879-880

DOI: 10.1093/bioinformatics/btr028

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

Journal article published in 2011 by Xin Wang ORCID, Camille Terfve, John C. Rose ORCID, Florian Markowetz
This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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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 , an integrated analysis pipeline for HTS data that contains over-representation analysis, gene set enrichment analysis, comparative gene set analysis and rich sub-network identification. HTSanalyzeR directly builds on commonly used pre-processing packages for HTS data and presents its statistical results as HTML pages and network plots.