Vencode

Minor changes and new funcionalities. This new version comes with improved scripts to generate pre-parsed data from the big FANTOM5 CAGE-seq data, improved documentation including the one submitted and hosted at https://vencode.readthedocs.io, and other minor changes.

This version now simplifies in many ways how to retrieve VEnCodes and VEnCodes using validated regulatory elements. You can now issue commands to the utility file process.py from the command-line to get VEnCodes. Moreover, internals_extensions.py contain a few wrappers around the main methods, that create a pipeline for easy VEnCode generation in your scripts.

This release now allows the users to use the algorithms developed for data that is not coming from the FANTOM5 CAGE-seq project.