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- Title
CARPET: a web-based package for the analysis of ChIP-chip and expression tiling data.
- Authors
Matteo Cesaroni; Davide Cittaro; Alessandro Brozzi; Pier Giuseppe Pelicci; Lucilla Luzi
- Abstract
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
- Subjects
BIOINFORMATICS software; GENE expression; CHROMATIN; PRECIPITATION (Chemistry); BIOTECHNOLOGY; GENETIC transcription; QUALITY control
- Publication
Bioinformatics, 2008, Vol 24, Issue 24, p2918
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btn542