CARPET specifications

Information


Unique identifier OMICS_26915
Name CARPET
Alternative name Collection of Automated Routine Programs for Easy Tilling
Interface Web user interface
Restrictions to use None
Output data A file of the peak’s coordinates and their corresponding score/P-value.
Output format GFF
Programming languages Perl, Python, R
Computer skills Basic
Stability No
Maintained No

Maintainer


This tool is not available anymore.

Information


Unique identifier OMICS_26915
Name CARPET
Alternative name Collection of Automated Routine Programs for Easy Tilling
Software type Application/Script
Interface Command line interface
Restrictions to use None
Output data A file of the peak’s coordinates and their corresponding score/P-value.
Output format GFF
Operating system Unix/Linux
Programming languages Perl, Python, R
Computer skills Advanced
Stability No
Maintained No

Versioning


No version available

Maintainer


This tool is not available anymore.

Publication for Collection of Automated Routine Programs for Easy Tilling

CARPET citations

 (2)
library_books

Combined ChIP Seq and transcriptome analysis identifies AP 1/JunD as a primary regulator of oxidative stress and IL 1β synthesis in macrophages

2013
BMC Genomics
PMCID: 3608227
PMID: 23398888
DOI: 10.1186/1471-2164-14-92

[…] filter out regions which showed no enrichment but had a high enough background for the algorithm to call peaks in. Peak regions were annotated using the gene intervals annotator (GIN) implemented in CARPET using a gene priority approach to give the associated transcript I.D., the associated gene feature and the distance of the peak to the nearest transcriptional start site []. HOMER was used to p […]

library_books

A Widespread Distribution of Genomic CeMyoD Binding Sites Revealed and Cross Validated by ChIP Chip and ChIP Seq Techniques

2010
PLoS One
PMCID: 3012110
PMID: 21209968
DOI: 10.1371/journal.pone.0015898

[…] Quantile normalization, peak detection, gene annotation, peak distribution was done using the CARPET tiling analysis software package . HLH-1 bound peaks and interval sequences were identified using the following parameters in the notator function: analysis type, p-value; percentile value, 0.9 […]

CARPET institution(s)
Department of Experimental Oncology, European Institute of Oncology, Milano, Italy; Cogentech, Consortium for Genomic Technologies, Milano, Italy; IFOM, FIRC Institute of Molecular Oncology Foundation, Milano, Italy
CARPET funding source(s)
Supported by the Italian Association for Oncology Research (OGCG1139).

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