HAMdetector: A Bayesian regression model that integrates information to detect HLA-associated mutations
Escape.jl (HAMdetector) is a julia 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:
- Linux 64-bit
- git
- Julia 1.6 or newer
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.
If you experience issues during the installation or usage of HAMdetector, please open an issue in this repository. Contributions in the form of suggestions, improvements to the documentation, or pull requests are extremely welcome.
The HAMdetector source code is distributed under a permissive MIT license (see file LICENSE).