Tool:Roakvar: do genomic variant analyses with R

Question

[Ryangguk Kim]

Roakvar is an R package for genomic variant analysis. It is an R wrapper for OakVar, a Python-based genomic variant analysis platform (OakVar is in turn further developed from OpenCRAVAT).

Without leaving the RStudio, VCF files can be annotated and the result can be pulled into an R data frame, for example.

See https://github.com/rkimoakbioinformatics/roakvar for Roakvar installation and usage, including the example.

See https://oakvar.readthedocs.io for OakVar installation and usage.

All CLI commands of OakVar is available as R functions through Roakvar, including a GUI server.

Comments and feedback are welcome.

[cpad0112]

For reference, oakvar (python) is fork of opencravat (variant interpretation software )

Answer 1

[Ryangguk Kim]

Roakvar v2.4.5 has been released, to match the newly released OakVar v2.4.5.

This version has improvements to meet CRAN's submission requirements including silent run by default and returning results instead of printing to stdout. As of now, still the best way to install Roakvar is

>devtools::install_github("rkimoakbioinformatics/roakvar")