epitopepredict - 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

- Jupyter Notebook
Published by dmnfarrell almost 6 years ago

epitopepredict - 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

- Jupyter Notebook
Published by dmnfarrell over 7 years ago

epitopepredict - 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

- Jupyter Notebook
Published by dmnfarrell about 8 years ago

epitopepredict - 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

- Jupyter Notebook
Published by dmnfarrell over 8 years ago

epitopepredict - 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.

- Jupyter Notebook
Published by dmnfarrell over 10 years ago