Metadata-Version: 2.1
Name: MAmotif
Version: 1.1.0
Summary: An integrative toolkit for detecting cell type-specific regulators
Home-page: https://github.com/shao-lab/MAmotif
Author: Hayden Sun
Author-email: sunhongduo@picb.ac.cn
License: BSD
Project-URL: Bug Tracker, https://github.com/shao-lab/MAmotif/issues
Project-URL: Documentation, https://mamotif.readthedocs.io
Project-URL: Source Code, https://github.com/shao-lab/MAmotif
Description: MAmotif
        =======
        
        |Documentation Status| |pypi| |license|
        
        .. |Documentation Status| image:: https://readthedocs.org/projects/mamotif/badge/?version=latest
           :target: https://mamotif.readthedocs.io/en/latest/?badge=latest
        .. |pypi| image:: https://img.shields.io/pypi/v/mamotif.svg
           :target: https://pypi.org/project/MAmotif/
        .. |license| image:: https://img.shields.io/pypi/l/MAmotif.svg
           :target: https://github.com/shao-lab/MAmotif/blob/master/LICENSE
        
        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
        --------
        
        .. image:: https://github.com/shao-lab/MAmotif/blob/master/docs/source/image/MAmotif_workflow.png
        
        Citation
        --------
        
        `Sun H, Wang J, Gong Z, Yao J, Wang Y, Xu J, Yuan GC, Zhang Y, Shao Z. Quantitative integration of epigenomic variation
        and transcription factor binding using MAmotif toolkit identifies an important role of IRF2 as transcription activator
        at gene promoters. Cell discovery. 2018 Jul 10;4(1):38. <https://www.nature.com/articles/s41421-018-0045-y>`__
        
        Installation
        ------------
        
        The latest release of MAmotif is available at `PyPI <https://pypi.org/project/MAmotif/>`__:
        
        .. code-block:: shell
        
            $ pip install mamotif
        
        Or you can install MAmotif via conda:
        
        .. code-block:: shell
        
            $ conda install -c bioconda mamotif
        
        
        Documentation
        -------------
        
        To see the full documentation of MAmotif, please refer to: http://mamotif.readthedocs.io/en/latest/
        
        License
        -------
        
        `BSD 3-Clause
        License <https://github.com/shao-lab/MAmotif/blob/master/LICENSE>`__
        
        
        
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: Unix
Classifier: Operating System :: POSIX
Classifier: Operating System :: MacOS
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.6
Provides-Extra: test
Provides-Extra: docs
