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

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


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.


Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatin Immunoprecipitation / methods*
  • Databases, Genetic
  • Gene Expression Profiling / methods*
  • Genome
  • Internet
  • Oligonucleotide Array Sequence Analysis / methods*
  • Software*
  • Transcription, Genetic