CRC

Core transcriptional regulatory circuitry analysis

Dependencies

The CRC software uses the following dependencies:

• Bamliquidator
• Samtools
• FIMO
• fasta-get-markov

Both FIMO and fasta-get-markov can be found in The MEME Suite.

Install

pip install git+https://github.com/linlabcode/CRC.git

Usage

As a command line tool:

crc -e <enhacer_text_file> -g <genome_build> -s <peaks_bed_file> -c <chromosomes_dir> -o <out_dir> -n <name>

As a python library:

import crc

crc.crc(enhancers, genome_input, chrom_path, output, analysis_name, bam=None, subpeak_file=None,
        mask_file=None, activity_path=None, const_extension=100, number=1, motifs=None,
        config='')

Authors

Charles Y. Lin Baylor College of Medicine

Jost V. Koren Baylor College of Medicine

Alexander J. Federation University of Washington

Donald R. Polaski