CRCmapper specifications

Unique identifier:
Software type:
Restrictions to use:
Input format:
txt, bam, bed
Output format:
Programming languages:
Registration required:
Core Regulatory Circuitries mapper
Command line interface
Input data:
An enhancer table generated with ROSE, a sorted indexed bam file for H3K27ac sequencing reads, the build of the genome to be used for the analysis, the bedfile of peaks output from MACS used to identify SE constituents.
Output data:
The results of the motif search from the FIMO program, location matrix, list of gene names for genes assigned to SEs, transcripts NMIDs for transcripts assigned to SEs, list of TFs gene names predicted to bind their own SE, DNA background sequence file, table containing the candidate TFs and the location of their associated SEs, all possible CRCs ranked based on the average frequency of occurrence of the TFs they contain across all the possible interconnected auto regulatory loops, list of genes considered expressed, list of transcripts considered expressed as explained in the reference above, SE constituent sequences, SE constituent sequences used with FIMO, TSS coordinates, DNA binding motif locations in extended enhancer constituents for this TF.
Operating system:
Unix/Linux, Mac OS
Computer skills:
FIMO, SAMtools


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CRCmapper distribution


CRCmapper support


  • Violaine Saint-AndrĂ© <>


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Whitehead Institute for Biomedical Research, Cambridge, MA, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA, USA

Funding source(s)

This work was supported by the Foundation for the National Institutes of Health grant HG002668, by a National Science Foundation graduate fellowship, and the Hope Funds for Cancer Research Grillo-Marxuach Family Fellow.

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