nyzhoulang / hlaclustrview

R package specialized in HLA typing clustering and visualization based on specific similarity metrics.

HLA typing clustering and visualization based on specific similarity metrics

The HLAClustRView package implements specialized similarity metrics that quantify the similarity between human leukocyte antigen (HLA) typing from multiple samples. Using these metrics, the package enables hierarchical cluster analysis and can bind RNA-seq expression (when available) to the clusters.

Goal

The HLA genes plays a primary biological role in the regulation of the immune system and in the outcomes of human organ transplantation. However, the official HLA typing format is tedious to process. So far, not much analysis has been done from the clustering perspective for this type of data. The goal of the HLAClustRView package is to implement appropriate similarity metrics on HLA typing to enable sample clustering and more complex analysis.

Description of Package Functionality

The vignette of the HLAClustRView package, which is a document that provides a task-oriented description of the package functionality, contains the most up-to-date information.

Package Details

• Version: 0.99.0
• Depends: R (>= 3.3)
• Imports: purrr, dplyr, tidyr, tibble, utils, methods, stringr, data.table
• Suggests: testthat, knitr, rmarkdown

Package Workflow

Citing

If you use the HLAClustRView package for a publication, we would ask you to cite the following:

Pascal Belleau, Adewunmi Adelaja, Astrid Deschênes, Santiago Medina, Nissim Ranade and Allissa Dillman (2018). HLAClustRView: HLA typing clustering and visualization based on specific similarity metrics. R package version 0.99.0.

Authors

Pascal Belleau, Adewunmi Adelaja, Astrid Deschênes, Santiago Medina, Nissim Ranade and Allissa Dillman

License

This package and the underlying HLAClustRView code are distributed under the MIT license. You are free to use and redistribute this software.

For more information on MIT license see: https://opensource.org/licenses/MIT

Bugs/Feature requests

If you have any bugs or feature requests, let us know.

Thanks!