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Bioinformatics. 2008 Dec 15;24(24):2918-20. doi: 10.1093/bioinformatics/btn542. Epub 2008 Oct 21.

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

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  • 1Department of Experimental Oncology, European Institute of Oncology, Via Ripamonti 435, 20141 Milano, Italy.



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.


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