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Bioinformatics Advance Access originally published online on January 25, 2009
Bioinformatics 2009 25(5):678-679; doi:10.1093/bioinformatics/btp014
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

RNAither, an automated pipeline for the statistical analysis of high-throughput RNAi screens

Nora Rieber 1,*, Bettina Knapp 1, Roland Eils 2 and Lars Kaderali 1

1Viroquant Research Group Modeling, University of Heidelberg, Bioquant BQ26, Im Neuenheimer Feld 267 and 2Theoretical Bioinformatics, German Cancer Research Center, 69120 Heidelberg, Germany

*To whom correspondence should be addressed.


  Abstract

Summary: We present RNAither, a package for the free statistical environment R which performs an analysis of high-throughput RNA interference (RNAi) knock-down experiments, generating lists of relevant genes and pathways out of raw experimental data. The library provides a quality assessment of the signal intensities, as well as a broad range of options for data normalization, different statistical tests for the identification of significant siRNAs, and a significance analysis of the biological processes involving corresponding genes. The results of the analysis are presented as a set of HTML pages. Additionally, all values and plots are available as either text files or pdf and png files.

Availability: http://bioconductor.org/

Contact: RNAither{at}gmx.de

Associate Editor: Joaquin Dopazo

Received on October 21, 2008; revised on November 27, 2008; accepted on January 1, 2009

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