devgru

A developmental R environment for a suite of GenomicRanges utilities

Installation

You can install the current development version of devgru with:

devtools::install_github("pblaney/devgru")
#BiocManager::install("pblaney/devgru")

Suite of Packages

The current suite of utilities for devgru can be quickly installed, if needed, and loaded with:

kit_loadout()

GenomicRanges Core

• BSgenome.Hsapiens.UCSC.hg38
• GenomicRanges
• GenomeInfoDb
• data.table
• mskilab-org/gUtils
• VariantAnnotation
• rtracklayer
• Biostrings
• S4Vectors

Utility Core

• dplyr
• stringr
• readr
• ggplot2
• ggsci
• paletter
• scico
• flextable
• mclust
• parallel
• doParallel
• foreach

Development tools

• Continuous code testing is possible thanks to GitHub actions through usethis, remotes, and rcmdcheck customized to use Bioconductor’s docker containers and BiocCheck.
• Code coverage assessment is possible thanks to codecov and covr.
• The documentation website is automatically updated thanks to pkgdown.
• The code is styled automatically thanks to styler.
• The documentation is formatted thanks to devtools and roxygen2.

This package was developed using biocthis.