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.
| Original language | English |
|---|---|
| Pages (from-to) | 2918-2920 |
| Number of pages | 3 |
| Journal | Bioinformatics |
| Volume | 24 |
| Issue number | 24 |
| DOIs | |
| Publication status | Published - Dec 2008 |
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ASJC Scopus subject areas
- Biochemistry
- Molecular Biology
- Computational Theory and Mathematics
- Computer Science Applications
- Computational Mathematics
- Statistics and Probability
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CARPET : A web-based package for the analysis of ChIP-chip and expression tiling data. / Cesaroni, Matteo; Cittaro, Davide; Brozzi, Alessandro; Pelicci, Pier Giuseppe; Luzi, Lucilla.
In: Bioinformatics, Vol. 24, No. 24, 12.2008, p. 2918-2920.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - CARPET
T2 - A web-based package for the analysis of ChIP-chip and expression tiling data
AU - Cesaroni, Matteo
AU - Cittaro, Davide
AU - Brozzi, Alessandro
AU - Pelicci, Pier Giuseppe
AU - Luzi, Lucilla
PY - 2008/12
Y1 - 2008/12
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=57349109349&partnerID=8YFLogxK
U2 - 10.1093/bioinformatics/btn542
DO - 10.1093/bioinformatics/btn542
M3 - Article
C2 - 18945685
AN - SCOPUS:57349109349
VL - 24
SP - 2918
EP - 2920
JO - Bioinformatics
JF - Bioinformatics
SN - 1367-4803
IS - 24
ER -