Base functions for bioinformatics and R package development.

Installation

Requirements: R >= 3.6, Bioconductor >= 3.10.

R method

if (!requireNamespace("remotes", quietly = TRUE)) {
    install.packages("remotes")
}
Sys.setenv(R_REMOTES_UPGRADE = "always")
# Set `GITHUB_PAT` in `~/.Renviron` if you get a rate limit error.
remotes::install_github("acidgenomics/basejump")

Here’s how to update to the latest version on GitHub:

Sys.setenv(R_REMOTES_UPGRADE = "always")
remotes::update_packages()

Always check that your Bioconductor installation is valid before proceeding.

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
BiocManager::valid()

Conda method

Configure Conda to use the Bioconda channels.

# Don't install recipe into base environment.
name="r-basejump"
conda create --name="$name" "$name"
conda activate "$name"
R

Docker method

image="acidgenomics/basejump"
workdir="/work"
docker pull "$image"
docker run -it \
    --volume="${PWD}:${workdir}" \
    --workdir="$workdir" \
    "$image" \
    R

References

The papers and software cited in our workflows are available as a shared library on Paperpile.