Metadata-Version: 2.1
Name: motifscan
Version: 1.3.0
Summary: A package for motif discovery and motif enrichment analysis
Home-page: https://github.com/shao-lab/MotifScan
Author: Hayden Sun
Author-email: sunhongduo@picb.ac.cn
License: BSD
Project-URL: Bug Tracker, https://github.com/shao-lab/MotifScan/issues
Project-URL: Documentation, https://motifscan.readthedocs.io
Project-URL: Source Code, https://github.com/shao-lab/MotifScan
Description: MotifScan
        =========
        
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           :target: https://pypi.org/project/motifscan/
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           :target: https://github.com/shao-lab/MotifScan/blob/master/LICENSE
        
        Introduction
        ============
        
        **Scan input genomic regions with known DNA motifs**
        
        Given a set of input genomic regions, MotifScan scans the sequences to
        detect the occurrences of known motifs. It can also applies a statistical test
        on each motif to check whether the motif is significantly over- or under-represented
        (enriched or depleted) in the input genomic regions compared to another set of control
        regions.
        
        Citation
        ========
        
        `Sun, H., Wang, J., Gong, Z. et al. 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 Discov 4, 38 (2018).`__
        
        .. __: https://doi.org/10.1038/s41421-018-0045-y
        
        Documentation
        =============
        
        To see the full documentation of MotifScan, please refer to: https://motifscan.readthedocs.io
        
        Installation
        ============
        
        The latest version release of MotifScan is available at
        `PyPI <https://pypi.python.org/pypi/motifscan>`__:
        
        ::
        
            $ pip install motifscan
        
        Or you can install MotifScan via conda:
        
        ::
        
            $ conda install -c bioconda motifscan
        
        Usage
        =====
        
        Install genome assemblies
        -------------------------
        
        Install from a remote database
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        You can download genome assemblies from the `UCSC`_ database.
        
        First, display all available genome assemblies:
        
        .. code-block:: shell
        
            $ motifscan genome --list-remote
        
        Then, install a genome assembly (e.g. hg19):
        
        .. code-block:: shell
        
            $ motifscan genome --install -n hg19 -r hg19
        
        Install with local files
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        To install a genome assembly locally, you have to prepare a FASTA file
        containing the genome sequences and a genome annotation file (refGene.txt).
        
        .. code-block:: shell
        
            $ motifscan genome --install -n hg19 -i <hg19.fa> -a <refGene.txt>
        
        
        Install and build motif sets
        ----------------------------
        
        Install from a remote database
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Users can install motif PFMs sets in the `JASPAR`_ 2020 database.
        
        First, display all available motif PFMs sets in JASPAR 2020:
        
        .. code-block:: shell
        
            $ motifscan motif --list-remote
        
        Then, install a JASPAR motif PFMs set (e.g. vertebrates_non-redundant):
        
        .. code-block:: shell
        
            $ motifscan motif --install -n <motif_set> -r vertebrates_non-redundant -g hg19
        
        
        Install with local files
        ^^^^^^^^^^^^^^^^^^^^^^^^
        
        Install a motif set with local PFMs file:
        
        .. code-block:: shell
        
           $ motifscan motif --install -n <motif_set> -i <pfms.jaspar> -g hg19
        
        Build PFMs for additional genome
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
        
        Build the motif PFMs set for another installed genome assembly hg38:
        
        .. code-block:: shell
        
           $ motifscan motif --build <motif_set> -g hg38
        
        Scanning Motifs
        ---------------
        
        After the data preparation steps, you can now scan a set of genomic regions to
        detect the occurrences of known motifs.
        
        .. code-block:: shell
        
           $ motifscan scan -i regions.bed -g hg19 -m <motif_set> -o <output_dir>
        
        .. _UCSC: https://genome.ucsc.edu/
        .. _JASPAR: http://jaspar.genereg.net/
        
        **Note:** Using -h/--help for the details of all arguments.
        
        
        License
        =======
        
        `BSD 3-Clause
        License <https://github.com/shao-lab/MotifScan/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
Description-Content-Type: text/x-rst
Provides-Extra: test
Provides-Extra: docs
