Pyproteome

Features

- Completed clustering module.
- Added much more extensive integration testing, fixing many py2 bugs.
- Re-organized analysis into package.
- Added code for normalizing across data sets with no shared channels.
- Cleared out old code for reading tab-delimited Discoverer exports.
- Save plots into organized folders.

Features

- Added pick_best_ptm option to DataSet, enabled by default. This selects
only the peptide with the best PTM assignment to be used for each scan. It
is recommended to disable this feature on large pS/T data sets.
- Sequence.\_\_contains\_\_ supports string arguments now.
- Added individual sample quantitations to write_full_tables()
- Automatically apply inter-normalization when merging multiple data sets.
- Filter by several new parameters.
- Added motifs, cluster, brainrnaseq modules.
- Added integration tests.
- Reorganized several analysis functions.
- Removed unused / untested enrichment module.

Bugfixes

- Fixed several runtime warnings from matplotlib / numpy / pandas.
- Fixed many py2 issues.

Bugfixes

- Fixed levels.get_channel_levels not displaying all histogram plots
- Cleared up clutter on analysis.volcano_plot

Features

- Drop notebook requirement down to just ipython.

Bugfixes

- Fixed truncation of x/y-axis ticks on volcano plots.

Features

- Added support for > 2 groups.
- Added support for inter-run normalization.

Bugfixes

- Too many bug-fixes to count.

Bugfixes

- Fixed uniprot needing to be installed separately.