This is the repository for the manuscript 'Prediction of HIV-1 sensitivity to broadly neutralizing antibodies shows a trend towards resistance over time', which proposes to use oligo kernel based SVMs to predict neutralization sensitivity or resistance of HIV-1 variants towards broadly neutralizing antibodies (bNAbs).
Manuscript authors: Anna Hake and Nico Pfeifer
In this repository you find:
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FinalModels.tar.gz: A tar gzipped folder containing everything to reproduce the prediction performances of our final models as well as the training samples and resampling instances to compare new methods to our method. It also contains a README file.
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TrendAnalysis.tar.gz: A tar gzipped folder containing everything to reproduce the trend analysis. It also contains a README file.
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The umbrella code for the trend analysis was originally downloaded from http://static.gest.unipd.it/~salmaso/web/springerbook.htm
Please let us know if you have any problems to reproduce our results or have any suggestions.
Disclaimer: The models are not for clinical usage! The models are only for academic use, with no warranty or liability.