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