Base functions for bioinformatics and R package development.

Installation

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.

conda install -c bioconda r-basejump

References

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