MAmotif
Introduction
MAmotif is used to compare two ChIP-seq samples of the same protein from different cell types or conditions (e.g. Mutant vs Wild-type) and identify transcriptional factors (TFs) associated with the cell-type biased binding of this protein as its co-factors, by using TF binding information obtained from motif analysis (or from other ChIP-seq data).
MAmotif automatically combines MAnorm model to perform quantitative comparison on given ChIP-seq samples together with Motif-Scan toolkit to scan ChIP-seq peaks for TF binding motifs, and uses a systematic integrative analysis to search for TFs whose binding sites are significantly associated with the cell-type biased peaks between two ChIP-seq samples.
When applying to ChIP-seq data of histone marks of regulatory elements (such as H3K4me3 for active promoters and H3K9/27ac for active promoter/enhancers), or DNase/ATAC-seq data, MAmotif can be used to detect cell-type specific regulators.
Workflow
Citation
Installation
The latest release of MAmotif is available at PyPI:
$ pip install mamotifOr you can install MAmotif via conda:
$ conda install -c bioconda mamotifDocumentation
To see the full documentation of MAmotif, please refer to: http://mamotif.readthedocs.io/en/latest/
License
1 maintainer
Metadata
1 maintainer
Release files for MAmotif 1.1.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
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| MAmotif-1.1.0.tar.gz | 4.7 MB | Details |
Release files / MAmotif-1.1.0.tar.gz
| Download URL | MAmotif-1.1.0.tar.gz |
|---|---|
| Size | 4.7 MB |
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