A robust model for quantitative comparison of ChIP-Seq data sets.
Project description
Introduction
ChIP-Seq is widely used to characterize genome-wide binding patterns of transcription factors and other chromatin-associated proteins. Although comparison of ChIP-Seq data sets is critical for understanding cell type-dependent and cell state-specific binding, and thus the study of cell-specific gene regulation, few quantitative approaches have been developed.
Here, we present a simple and effective method, MAnorm, for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.
Citation
Documentation
To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io/en/latest/
Installation
The latest version release of MAnorm is available at PyPI:
$ pip install manorm
Or you can install MAnorm via conda:
$ conda install -c bioconda manorm
MAnorm uses setuptools for installation from source code. The source code of MAnorm is hosted on GitHub: https://github.com/shao-lab/MAnorm
You can clone the repo and execute the following command under source directory:
$ python setup.py install
Usage
$ manorm --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed -o sample1_vs_sample2
Note: Using -h/–help for the details of all arguments.
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