v0.6.0

• fixes to mapping step to correct bug in mapping from remaining reads
• updated novel module to run with current versions of joblib, sklearn
• added training data files for novel model, now trained on first use

v0.5.0

• fixes to work with python 3 properly
• snap now works
• updated to use mirbase release 22
• sphinx docs added
• can run novel predictions in parallel
• some fixes to precursor generation
• removed bedtools dependency
• improvements to plots

v0.4.0

Differential expression now works from command line.

• added test trf module for trna fragment counting, not yet fully implemented
• differential expression improved output
• implemented separate limma and edgeR for de analysis

v0.3.0

• Added missing code for isomir counting
• Fix for problem with treating filenames as strings in python 2 when calling HTSeq
• Some changes to output for mirna counting
• Can run a basic test from cmd line
• Tested to work on OSX

v0.2.1

Mostly minor fixes from 0.2.0.

• Can do feature counting from command line
• Fixed to allow split counts for multi mappers
• Changes to novel report output
• Removed biopython dep
• Removed some mpl imports

v0.2.0

First stable release for use. No version of the code on github prior to this release should be considered usable since a lot of changes to the modules has been done.

Changes

• Added command line interface
• Use of config file for cmd line
• Re-arrangement of modules
• Added feature counting
• Native mirna/isomir counting
• Novel mirna discovery added