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        "author": "Hayden Sun",
        "author_email": "sunhongduo@picb.ac.cn",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 3 - Alpha",
            "Environment :: Console",
            "Intended Audience :: Education",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Operating System :: POSIX :: Linux",
            "Operating System :: Unix",
            "Programming Language :: Python",
            "Programming Language :: Python :: 2",
            "Programming Language :: Python :: 2.7",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "MAmotif\n=======\n\n|travis-ci| |Documentation Status| |pypi| |license|\n\n.. |travis-ci| image:: https://travis-ci.org/shao-lab/MAmotif.svg?branch=master\n   :target: https://travis-ci.org/shao-lab/MAmotif\n.. |Documentation Status| image:: https://readthedocs.org/projects/mamotif/badge/?version=latest\n   :target: http://mamotif.readthedocs.io/en/latest/?badge=latest\n.. |pypi| image:: https://img.shields.io/pypi/v/mamotif.svg\n   :target: https://pypi.python.org/pypi/mamotif\n.. |license| image:: https://img.shields.io/pypi/l/MAmotif.svg\n   :target: https://github.com/shao-lab/MAmotif/blob/master/LICENSE\n\nIntroduction\n------------\n\n**MAmotif** is used to compare two ChIP-seq samples of the same protein from different cell types or conditions\n(e.g. Mutant vs Wild-type) and **identify transcriptional factors (TFs) associated with the cell-type biased binding**\nof this protein as its **co-factors**, by using TF binding information obtained from motif analysis\n(or from other ChIP-seq data).\n\nMAmotif automatically combines **MAnorm** model to perform quantitative comparison on given ChIP-seq samples together\nwith Motif-Scan toolkit to scan ChIP-seq peaks for **TF binding motifs**, and uses a systematic integrative analysis to\nsearch for TFs whose binding sites are significantly associated with the cell-type biased peaks between two ChIP-seq samples.\n\nWhen applying to ChIP-seq data of histone marks of regulatory elements (such as H3K4me3 for active promoters and\nH3K9/27ac for active promoter/enhancers), or DNase/ATAC-seq data, MAmotif can be used to detect **cell-type specific regulators**.\n\nWorkflow\n--------\n\n.. image:: https://github.com/shao-lab/MAmotif/blob/master/docs/source/image/MAmotif_workflow.png\n\nDocumentation\n-------------\n\nTo see the full documentation of MAmotif, please refer to: http://mamotif.readthedocs.io/en/latest/\n\nInstallation\n------------\n\nThe latest release of MAmotif is available at `PyPI <https://pypi.python.org/pypi/mamotif>`__:\n\n::\n\n    $ pip install mamotif\n\nOr you can install MAmotif via conda:\n\n::\n\n    $ conda install -c bioconda mamotif\n\nMAmotif uses `setuptools <https://setuptools.readthedocs.io/en/latest/>`__ for installation from source code.\nThe source code of MAmotif is hosted on GitHub: https://github.com/shao-lab/MAmotif\n\nYou can clone the repo and execute the following command under source directory:\n\n::\n\n    $ python setup.py install\n\nGalaxy Installation\n-------------------\n\n**WIP!**\n\n\nUsage\n-----\n\nYou need to build some prerequisites before running MAmotif:\n\nBuild genomes\n^^^^^^^^^^^^^\n\nPreprocess sequences and genome-wide nucleotide frequency for the corresponding genome assembly.\n\n::\n\n    $ genomecompile [-h] [-v] -G hg19.fa -o hg19_genome\n\n**Note:** You only need to run this command once for each genome\n\nBuild motifs (Optional)\n^^^^^^^^^^^^^^^^^^^^^^^\n\n**Note:** MAmotif provides some preprocessed motif PWM files under **data/motif** of the MotifScan package.\n\nYou can download it by::\n\n    $wget --no-check-certificate https://github.com/shao-lab/MAmotif/raw/master/data/motif.tar.gz\n\nBuild motif PWM/motif-score cutoff for custom motifs that are not included in our pre-complied motif collection:\n\n::\n\n    $ motifcompile [-h] [-v] \u2013M motif_pwm_demo.txt \u2013g hg19_genome -o hg19_motif\n\nrun MAmotif\n^^^^^^^^^^^\n\n::\n\n    $ mamotif --p1 sample1_peaks.bed --p2 sample2_peaks.bed --r1 sample1_reads.bed --r2 sample2_reads.bed -g hg19_genome\n    \u2013m hg19_motif_p1e-4.txt -o sample1_vs_sample2\n\n**Note:** Using -h/--help for the details of all arguments.\n\nOutput of MAmotif\n-----------------\n\nAfter finished running MAmotif, all output files will be written to the directory you specified with \"-o\" argument.\n\nMain output\n^^^^^^^^^^^\n\n::\n\n    1.Motif Name\n    2.Target Number: Number of motif-present peaks\n    3.Average of Target M-value: Average M-value of motif-present peaks\n    4.Deviation of Target M-value: M-value Std of motif-present peaks\n    5.Non-target Number: Number of motif-absent peaks\n    6.Average of Non-target M-value: Average M-value of motif-absent peaks\n    7.Deviation of Non-target M-value: M-value Std of motif-absent peaks\n    8.T-test Statistics: T-Statistics for M-values of motif-present peaks against motif-absent peaks\n    9.T-test P-value: Right-tailed P-value of T-test\n    10.T-test P-value By Benjamin correction\n    11.RanSum-test Statistics\n    12.RankSum-test P-value\n    13.RankSum-test P-value By Benjamin correction\n    14.Maximal P-value: Maximal corrected P-value of T-test and RankSum-test\n\nMAnorm output\n^^^^^^^^^^^^^\n\nMAmotif will invoke MAnorm and output the normalization results and MA-plot for samples under comparison.\n\n\nMotifScan output\n^^^^^^^^^^^^^^^^\n\nMAmotif will also output tables to summarize the enrichment of motifs and the motif target number and motif-score\nof each peak region.\n\nIf you specified \"-s\" with MAmotif, it will also output the genome coordinates of every motif target site.\n\nExample Usage\n-------------\n\nHere we provide a step-by-step instruction on how to use MAmotif to find candidate cell-type specific regulators\nassociated with certain histone modifications.\n\nWe take the H3K4me3 analysis between adult and fetal ProES in MAmotif paper as an example:\n\n1. Install MAmotif::\n\n    $pip install mamotif\n    $conda install -c bioconda mamotif\n\n2. Download all data MAmotif needs::\n\n    $mkdir MAmotif_demo\n    $cd MAmotif_demo\n    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908038/suppl/GSM908038_H3K4me3-F_peaks.bed.gz\n    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908039/suppl/GSM908039_H3K4me3-A_peaks.bed.gz\n    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908038/suppl/GSM908038_H3K4me3-F.bed.gz\n    $wget ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM908nnn/GSM908039/suppl/GSM908039_H3K4me3-A.bed.gz\n    $gzip -d *gz\n\n    Remove the header line and ribosomal reads (You do not need to do this for modern ChIP-seq mapping softwares)\n    $sed -i '1d' GSM908038_H3K4me3-F.bed\n    $sed -i '1d' GSM908039_H3K4me3-A.bed\n    $sed -i '8986927,$d' GSM908039_H3K4me3-F.bed\n    $sed -i '14916308,$d' GSM908039_H3K4me3-A.bed\n\n    Substitute space into tab for bed files (You do not need to do this for your own bed files are tab-separated)\n    $sed -i \"s/ /\\t/g\" GSM908038_H3K4me3-F.bed\n    $sed -i \"s/ /\\t/g\" GSM908039_H3K4me3-A.bed\n\n\n3. Build for genome sequences::\n\n    $mkdir genome\n    $cd genome\n    $wget http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/chromFa.zip\n    $unzip chromFa.zip\n    $cat *fa > hg18.fa\n    $genomecompile -G hg18.fa -o hg18\n    $cd ..\n\n4. Build for motif PWM (Optional)\n\nThe motif matrix file which containing the motif score cutoff is already packaged under /data directory under MotifScan package.\n\nYou can download it by::\n\n    $wget --no-check-certificate https://github.com/shao-lab/MAmotif/raw/master/data/motif.tar.gz\n\nIf you want you compile for your custom motifs, please run the following commands::\n\n    $mkdir motif\n    $cd motif\n    $wget http://jaspar2016.genereg.net/html/DOWNLOAD/JASPAR_CORE/pfm/nonredundant.tar.gz\n    $tar -xzvf nonredundant.tar.gz\n    $motifcompile -M nonredundant/pfm_vertebrates.txt -g ../genome/hg18 -o hg18_jaspar2016_nonredundant_vertebrates\n    $cd ..\n\n5. Run MAmotif::\n\n   $mamotif --p1 GSM908039_H3K4me3-A_peaks.bed --p2 GSM908038_H3K4me3-F_peaks.bed --r1 GSM908039_H3K4me3-A.bed --r2 GSM908038_H3K4me3-F.bed -g genome/hg18 -m motif/hg18_jaspar2016_nonredundant_vertebrates_1e-4.txt -o AvsF_H3K4me3_MAmotif\n\n6. Check the output of MAmotif\n\n\nLicense\n-------\n\n`BSD 3-Clause\nLicense <https://github.com/shao-lab/MAmotif/blob/master/LICENSE>`__",
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