HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations

License: MIT

Escape.jl (HAMdetector) is a software package for identifying HLA associated substitutions based on annotated sequence data (aligned viral sequences paired to host HLA class I data).

HAMdetector makes use of information from epitope prediction via MHCflurry 2.0 and phylogeny (based on RAxML-NG). The model is fit using Stan.

See the documentation:

Software requirements

  • Linux 64-bit
  • Julia 1.6 or newer

Installation

In the Julia REPL, switch to Pkg-mode by typing the ] character. Then add HAMdetector_registry to your registry and install the Escape package:

pkg> registry add https://github.com/HAMdetector/HAMdetector_registry.git
pkg> add Escape

To make sure that HAMdetector was installed correctly, a large suite of unit tests can be run with ] test Escape.

Reporting Issues and Contributions

If you experience issues during installation or usage HAMdetector, please open an issue in this repository. Contributions in the form of suggestions, improvements to the documentation or pull requests are extremely welcome.

License

The HAMdetector source code is distributed under a permissive MIT license (see file LICENSE).