v0.5.0

Changes:

• replaced tornado web app with panel dashboard
• added sequence plot with Bokeh
• added limit kwd to promiscuous_binders
• fix to netmhciipan read_results
• changed cpus to threads kwd
• fixed position value in results dataframe
• improvements to basicmhc1 predictor
• changed cpus to threads kwd
• updated netmhcpan to support 4.1b
• removed refs to Bio Alphabet

v0.4.0

Changes:

• major changes to neoepitope routines
• changes to app outputs
• added netmhcpan predictor
• added basicmhc1 predictor
• updated notebook examples
• fixes for python 3
• snap mostly works

v0.3.0

This release adds an initial neo-epitope prediction workflow. Methods have been refactored to use underscore names.

Changes:

• renamed some predictor class methods
• can run predict_peptides in parallel
• changed all class methods to use underscore convention
• added neo module for neo-epitope prediction pipeline
• added sphinx documentation
• snap package now contains all required libraries
• fixed netmhciipan predictor
• default config file in home dir for paths
• changes default cutoff method for binders to use pre-defined quantiles for cutoffs
• simplified web interface

v0.2.0

This release reflects many changes to the code and is not compatible with 0.1. This includes a new command line usage tool and a web application.

Changes:

• now works with python >=2.7 and >=3.4
• changed module level methods to use underscore style
• added snapcraft script
• added mhcflurry predictor
• added multi threaded predictions
• IEDB prediction tools now largely work correctly
• preset alleles added
• new command line interface
• web app for viewing results with further uses planned

v0.1.0

This is an initial release. This library has now been renamed from mhcpredict to epitopepredict. In the future more general usage is planned beyond use of MHC binding prediction methods.