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.
To see the full documentation of MAnorm, please refer to: http://manorm.readthedocs.io
The latest release of MAnorm is available at PyPI:
$ pip install manorm
Or you can install MAnorm via conda:
$ conda install -c bioconda manorm
MAnorm is also available on Galaxy, you can incorporate MAnorm into your own Galaxy instance.
Please search and install MAnorm via the Galaxy Tool Shed.
$ manorm --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed --n1 name1 --n2 name2 -o output_dir
Note: Using -h/--help for the details of all arguments.