Base functions for bioinformatics and R package development.

Installation

Requirements: R >= 4.0, Bioconductor >= 3.11.

R method

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "basejump",
    repos = c(
        "r.acidgenomics.com",
        BiocManager::repositories()
    )
)

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/r-basejump"
workdir="/mnt/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.