CRCmapper specifications


Unique identifier OMICS_19254
Name Core Regulatory Circuitries mapper
Software type Package/Module
Interface Command line interface
Restrictions to use None
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.
Input format txt, bam, bed
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.
Output format txt,gff,meme,bed,fa
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Stability Stable
Requirements FIMO, SAMtools
Registration required No
Maintained Yes



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  • person_outline Violaine Saint-AndrĂ© <>

CRCmapper article

CRCmapper institution(s)
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
CRCmapper 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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