GimmeMotifs is a motif prediction pipeline.
Project description
GimmeMotifs
===========
|bioconda-badge| |PyPI version| |Build Status| |Code Health|
Suite of motif tools, including a motif prediction pipeline for ChIP-seq
experiments.
See `full GimmeMotifs
documentation <http://gimmemotifs.readthedocs.org/>`__ for detailed
installation instructions and usage examples.
Easy installation
-----------------
The most straightforward way to install GimmeMotifs is via
`conda <https://docs.continuum.io/anaconda/>`__ using the
`bioconda <https://bioconda.github.io/>`__ channel.
``$ conda install gimmemotifs -c bioconda -c R``
Quick start
-----------
Download a genome
~~~~~~~~~~~~~~~~~
Create a directory to store genome files.
``$ mkdir $HOME/genomes/``
To download and index a genome (all UCSC-supported genomes):
``$ gimme genome $HOME/genomes/ hg38``
Alternatively, you can index a genome directory with chromosome FASTA
files on your computer.
``$ gimme index /usr/share/genomes/hg19 hg19``
Predict some motifs:
~~~~~~~~~~~~~~~~~~~~
``$ gimme motifs my_peaks.bed -g hg38 -n my_motifs``
Frequently Asked Questions (FAQ)
--------------------------------
I get the following error: "Invalid value for background argument".
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Currently, this is a bug in the default configuration file. Run
``gimme motifs`` with the additional argument ``-b gc,random``.
.. |bioconda-badge| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
:target: http://bioconda.github.io
.. |PyPI version| image:: https://badge.fury.io/py/gimmemotifs.svg
:target: https://badge.fury.io/py/gimmemotifs
.. |Build Status| image:: https://travis-ci.org/simonvh/gimmemotifs.svg?branch=master
:target: https://travis-ci.org/simonvh/gimmemotifs
.. |Code Health| image:: https://landscape.io/github/simonvh/gimmemotifs/master/landscape.svg?style=flat
:target: https://landscape.io/github/simonvh/gimmemotifs/master
===========
|bioconda-badge| |PyPI version| |Build Status| |Code Health|
Suite of motif tools, including a motif prediction pipeline for ChIP-seq
experiments.
See `full GimmeMotifs
documentation <http://gimmemotifs.readthedocs.org/>`__ for detailed
installation instructions and usage examples.
Easy installation
-----------------
The most straightforward way to install GimmeMotifs is via
`conda <https://docs.continuum.io/anaconda/>`__ using the
`bioconda <https://bioconda.github.io/>`__ channel.
``$ conda install gimmemotifs -c bioconda -c R``
Quick start
-----------
Download a genome
~~~~~~~~~~~~~~~~~
Create a directory to store genome files.
``$ mkdir $HOME/genomes/``
To download and index a genome (all UCSC-supported genomes):
``$ gimme genome $HOME/genomes/ hg38``
Alternatively, you can index a genome directory with chromosome FASTA
files on your computer.
``$ gimme index /usr/share/genomes/hg19 hg19``
Predict some motifs:
~~~~~~~~~~~~~~~~~~~~
``$ gimme motifs my_peaks.bed -g hg38 -n my_motifs``
Frequently Asked Questions (FAQ)
--------------------------------
I get the following error: "Invalid value for background argument".
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Currently, this is a bug in the default configuration file. Run
``gimme motifs`` with the additional argument ``-b gc,random``.
.. |bioconda-badge| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat
:target: http://bioconda.github.io
.. |PyPI version| image:: https://badge.fury.io/py/gimmemotifs.svg
:target: https://badge.fury.io/py/gimmemotifs
.. |Build Status| image:: https://travis-ci.org/simonvh/gimmemotifs.svg?branch=master
:target: https://travis-ci.org/simonvh/gimmemotifs
.. |Code Health| image:: https://landscape.io/github/simonvh/gimmemotifs/master/landscape.svg?style=flat
:target: https://landscape.io/github/simonvh/gimmemotifs/master
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