Epitopepredict

removed refs to Bio Alphabet

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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

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major changes to neoepitope routines
some changes to app outputs
added netmhcpan predictor
added basicmhc1 predictor
updated notebook examples
neoepitope scoring model
fixes for python 3

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renamed some predictor class methods
can run predict_peptides in parallel
added mhcnuggets predictor class
changed all class methods to use underscore convention
added sphinx documentation
added neo module for neo-epitope prediction pipeline
snap package now builds with some predictors built in
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

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rewrote much of previous API
now works with python >=2.7 and >=3.4
changed module level methods to use underscore style
new command line interface
added snapcraft script
added mhcflurry predictor
added ability to run parallel predictions
IEDB prediction tools now work correctly
preset alleles added