=================================================== GimmeMotifs for transcription factor motif analysis =================================================== What is GimmeMotifs? -------------------- GimmeMotifs is an analysis framework for transcription factor motif analysis written in Python. It contains command-line scripts to predict *de novo* motifs, scan for known motifs, identify differential motifs, calculate motif enrichment statistics, plot sequence logos and more. In addition, all this functionality is available from a Python API. GimmeMotifs is free and open source research software. If you find it useful please cite our paper: - Bruse N and van Heeringen SJ, **GimmeMotifs: an analysis framework for transcription factor motif analysis**, bioRxiv, 2018. https://www.biorxiv.org/content/10.1101/474403v1.full. `doi: 10.1101/474403 `_. - van Heeringen SJ and Veenstra GJC, **GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments**, Bioinformatics. 2011 Jan 15;27(2):270-1. `doi: 10.1093/bioinformatics/btq636 `_. Getting started --------------- * The easiest way to :ref:`install` GimmeMotifs is using bioconda_ on Linux or Mac. From version 0.13.0 only Python 3 (>= 3.8) is supported. * Have a look at these :ref:`simple examples` to get a taste of what is possible. * Check out the more detailed :ref:`tutorials`. * Full command-line reference can be found :ref:`here`. * There's also an :ref:`API documentation`. Get help -------- * First, check the :ref:`FAQ` for common issues. * The preferred way to get support is through the `Github issues`_ page. * Finally, you can reach me by mail_ or via twitter_. .. _`Github issues`: https://github.com/vanheeringen-lab/gimmemotifs/issues .. _bioconda: https://bioconda.github.io/ .. _mail: simon.vanheeringen@gmail.com .. _twitter: https://twitter.com/svheeringen Full contents ------------- .. toctree:: :maxdepth: 2 installation overview examples tutorials reference api faq acknowledgments