Skip to content

R front-end for the Practical Haplotype Graph (PHG)

License

Apache-2.0, Apache-2.0 licenses found

Licenses found

Apache-2.0
LICENSE
Apache-2.0
LICENSE.md
Notifications You must be signed in to change notification settings

maize-genetics/rPHG

rPHG

Life Cycle Status R-CMD-check codecov DOI

Objective

rPHG is a system to interact with and retrieve information from a Practical Haplotype Graph (PHG) - a general, graph-based, computational framework for genotype inference. This is accomplished by leveraging the Breeding and PHG APIs.

Citation

To cite rPHG, please use the following citation:

Bradbury et al. (2022). The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation. Bioinformatics, 38(15), 3698--3702, https://doi.org/10.1093/bioinformatics/btac410

Installation

If you do not have experience working with and setting up rJava with your R installation, it is recommended that you read the long-form documentation. This walkthrough can be found here. If you are already fairly comfortable working with Java JDK and rJava, you can follow the following commands.

Package source code can be installed directly from this BitBucket repository using the devtools package:

if (!require("devtools")) install.packages("devtools")
devtools::install_github(repo = "maize-genetics/rPHG")

About

R front-end for the Practical Haplotype Graph (PHG)

Resources

License

Apache-2.0, Apache-2.0 licenses found

Licenses found

Apache-2.0
LICENSE
Apache-2.0
LICENSE.md

Stars

Watchers

Forks

Packages

No packages published

Languages