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 in order to build reproducible and flexible NGS analysis pipelines.
- Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012.
User guide and reference
.. toctree:: :numbered: :maxdepth: 3 getting_started.rst gene-regulation_library.rst dependencies.rst tutorials.rst environments.rst snakemake.rst wiki.rst