Description

bbcflib is a set of Python modules for accessing facilities used by the Bioinformatics and Biostatistics Core Facility (BBCF) at the EPFL. It provides modules for BBCF’s

  • GenRep (genome data repository),
  • the LIMS of the DNA Array Facilities at UNIL and UNIGE,
  • the standard frontend code for workflows written by Fabrice David,
  • sending job completion emails.
  • the GDV api for viewing genome tracks
  • mapseq to map reads to reference genomes
  • chipseq to run ChIP-seq analyses
  • rnaseq to map reads to reference transcriptomes and compute statistics of differential expression
  • snp to search for SNP with respect to a reference genome

All the functionality can be imported with:

import bbcflib.module

where module is one of:

Installation

bbcflib requires:

Latest source code is available from GitHub:

http://github.com/bbcf/bbcflib

by clicking on “Downloads”, or by cloning the git repository with:

$ git clone https://github.com/bbcf/bbcflib.git

License

bbcflib is released under the GNU General Public License 3.0. A copy of this license is in the LICENSE.txt file.

Table Of Contents

Previous topic

Mapping

Next topic

Module: bbcflib.common

This Page

Websites