Publicly available looper-compatible pipelines
Pipelines on this list should be runnable on projects defined using the standard PEP project format.
- https://github.com/epigen/open_pipelines - A collection of pipelines to process diverse sequencing data types, including ATAC-seq, RNA-seq, and others.
- https://github.com/databio/rnapipe - A set of pipelines specifically for processing RNA.
- https://github.com/databio/dnameth_pipelines - Pipelines for Whole Genome and Reduced Representation Bisulfite Sequencing (WGBS and RRBS).
- https://github.com/databio/HiChIP-pipeline - A looper pipeline for processing HiChIP data (wrapper of HiC-pro).
- http://code.databio.org/PEPATAC - An ATAC-seq pipeline
Please contribute any new looper compatible pipelines to this list via pull request.