Pyproteome

Changes

- Improved the documentation substantially.
- Removed unused BCA and QC modules.

Changes

- Fixed installing pyproteome on a vanilla python base.

Features

- Added binomial enrichment plots for pathway analysis.
- Added protein-peptide mapping display.
- Added MERGE_UNDERLABELED option to combine peptides with variable TMT labeling.
- Added pathway analysis module for fetching Gene Ontology terms.
- Added pathway analysis module for partial least square regression (PLSR) analyses.
- Added pairwise correlation function.
- Improved speed and modularity of data normalization.
- Updated MSigDB to v7.1.
- Cleaned up the display of several plotting functions.

Changes

- Use log2 Fold Change when calling PHOTON.
- Added `save_cols` argument to `tables.write_full_tables()` to save custom columns.
- Added the ability to use multiple control groups to `DataSet.norm_cmp_groups()`.

Bug fixes

- Fixed several data mutability bugs.
- Fixed bugs with phosphosite localization with different versions of PhosphoRS/ptmRS.

Features

- Added module for CONSTANd normalization.
- Significant speed and memory improvements with large data sets.
- Fixed several bugs when using groups with duplicated sample IDs.
- Fixed plotting bugs when using data sets with duplicate samples / groups.
- Added Hensen et al. backend to brainrnaseq.
- Updated PTMSigDB to 1.9.1.

Bug fixes

- Fixed minor bugs in figure layouts.

Features

- Added support for ProteomeDiscoverer 2.2.
- Improved the layout of several analysis figures.
- Added cell type, gene ontology enrichment functions.