This git repository holds shared code for the analysis of Next Generation Sequencing data related to gene regulation: ChIP-seq, RNA-seq, and related technologies.
It was developed as part of the France Genomique Workpackage 2.6: Gene expression regulation.
One of the key goals is to ensure portability and re-usability of the code.
We have chosen to use the Snakemake workflow management system[1] in order to build reproducible and flexible NGS analysis pipelines.
- Claire Rioualen claire.rioualen@inserm.fr
- Jacques van Helden Jacques.van-helden@univ-amu.fr
- Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012.
.. toctree::
:numbered:
:maxdepth: 3
getting_started.rst
gene-regulation_library.rst
dependencies.rst
tutorials.rst
environments.rst
snakemake.rst
wiki.rst