README.md

In NCBI-Hackathons/HLAClustRView: 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 play 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 specific 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, stats, ComplexHeatmap, graphics, rlang
• Suggests: testthat, knitr, rmarkdown, circlize, BiocStyle

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](http://ca.linkedin.com/in/pascalbelleau "Pascal Belleau"), [Adewunmi Adelaja](https://www.linkedin.com/in/adewunmi-adelaja-2b3b1635/ "Adewunmi Adelaja"), [Astrid Deschênes](https://www.linkedin.com/in/astriddeschenes "Astrid Deschênes"), [Santiago Medina](https://github.com/santiago1234), [Nissim Ranade](https://www.linkedin.com/in/nissim-ranade-4029b3b5 "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](https://opensource.org/licenses/MIT) ## Bugs/Feature requests ## If you have any bugs or feature requests, [let us know](https://github.com/NCBI-Hackathons/Integrating-HLA-typing-methods-and-RNA-seq/issues). Thanks!

NCBI-Hackathons/HLAClustRView documentation built on Nov. 22, 2019, 6:11 a.m.