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Bioinformatics. 2014 Sep 1;30(17):2519-20. doi: 10.1093/bioinformatics/btu334. Epub 2014 May 14.

RNASeqExpressionBrowser--a web interface to browse and visualize high-throughput expression data.

Author information

1
Institute for Bioinformatics and Systems Biology (IBIS), Helmholtz Center Munich, National Research Center for Environment and Health, 85764 Neuherberg, Germany.

Abstract

MOTIVATION:

RNA-seq techniques generate massive amounts of expression data. Several pipelines (e.g. Tophat and Cufflinks) are broadly applied to analyse these datasets. However, accessing and handling the analytical output remain challenging for non-experts.

RESULTS:

We present the RNASeqExpressionBrowser, an open-source web interface that can be used to access the output from RNA-seq expression analysis packages in different ways, as it allows browsing for genes by identifiers, annotations or sequence similarity. Gene expression information can be loaded as long as it is represented in a matrix-like format. Additionally, data can be made available by setting up the tool on a public server. For demonstration purposes, we have set up a version providing expression information from the barley genome.

AVAILABILITY AND IMPLEMENTATION:

The source code and a show case are accessible at http://mips.helmholtz-muenchen.de/plant/RNASeqExpressionBrowser/.

PMID:
24833805
DOI:
10.1093/bioinformatics/btu334
[Indexed for MEDLINE]

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