rTASSEL

rTASSEL is an R-based front-end for accessing key TASSEL 5 methods and tools. This allows users to run powerful TASSEL 5 analyses within a unified R workflow, without switching between environments. rTASSEL also offers performance and feature advantages over other R packages. See these benchmarks for details.

Citation

To cite rTASSEL, please use the following citation:

Monier et al., (2022). rTASSEL: An R interface to TASSEL for analyzing genomic diversity. Journal of Open Source Software, 7(76), 4530, https://doi.org/10.21105/joss.04530

Installation

Stable release

# install.packages("pak")
pak::pak("maize-genetics/rTASSEL@v0.12.0")

Developmental version

# install.packages("pak")
pak::pak("maize-genetics/rTASSEL")

Note

Since rTASSEL uses rJava, you will need a working version of Java (≥ 8).

Mac/Linux users: you may need to run R CMD javareconf if you run into issues with installing rJava via pak. More installation tips can be found here.

I also recommend checking out Egor Kotov's rJavaEnv package to further automate your R to Java setup!

Docker

To avoid configuring Java and R locally, you can build a container from the docker/Dockerfile in this repository. See the installation article for build instructions, docker run examples, and RStudio Server usage.

Demo

If you want to test out what this package does but do not want to install it locally, we have set up an interactive Jupyter notebook detailing the walkthrough of rTASSEL on Binder. The Binder link can be accessed through the Binder icon on this page or by clicking here.

Getting help

For an overview of available functions, use the following command:

help(package = "rTASSEL")

If you need a walkthrough for potential pipelines, long-form documentation can be found on our website including a getting started article.

If you would like to study a function in full, refer to the R documentation by using ?<function> in the console, where <function> is an rTASSEL-based function.