Journal Article

CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data

Matteo Cesaroni, Davide Cittaro, Alessandro Brozzi, Pier Giuseppe Pelicci and Lucilla Luzi

in Bioinformatics

Volume 24, issue 24, pages 2918-2920
Published in print December 2008 | ISSN: 1367-4803
Published online October 2008 | e-ISSN: 1460-2059 | DOI: http://dx.doi.org/10.1093/bioinformatics/btn542
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data

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Summary: CARPET (collection of automated routine programs for easy tiling) is a set of Perl, Python and R scripts, integrated on the Galaxy2 web-based platform, for the analysis of ChIP-chip and expression tiling data, both for standard and custom chip designs. CARPET allows rapid experimental data entry, simple quality control, normalization, easy identification and annotation of enriched ChIP-chip regions, detection of the absolute or relative transcriptional status of genes assessed by expression tiling experiments and, more importantly, it allows the integration of ChIP-chip and expression data. Results can be visualized instantly in a genomic context within the UCSC genome browser as graph-based custom tracks through Galaxy2. All generated and uploaded data can be stored within sessions and are easily shared with other users.

Availability: http://bio.ifom-ieo-campus.it/galaxy

Contacts: matteo.cesaroni@ifom-ieo-campus.it; lucilla.luzi@ifom-ieo-campus.it

Journal Article.  1587 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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