Base functions for bioinformatics and R package development.

Installation

This is an R package.

Bioconductor

We recommend installing the package with BiocManager.

if (!require("BiocManager")) {
    install.packages("BiocManager")
}
BiocManager::install(
    pkgs = c(
        "devtools",
        "remotes",
        "GenomeInfoDbData"
    )
)
BiocManager::install(
    pkgs = "steinbaugh/basejump",
    dependencies = c("Depends", "Imports", "Suggests")
)

For R < 3.5, BiocManager is not supported. Use BiocInstaller::biocLite() instead of BiocManager::install(). This requires sourcing the legacy Bioconductor biocLite.R script.

# try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")

conda

Configure conda to use the bioconda channels.

conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

To avoid version issues, your .condarc file should only contain the following channels, in this order:

channels:
  - bioconda
  - conda-forge
  - defaults

We recommend installing into a clean conda environment:

conda create --name r
conda activate r

Launch R and check that it is set up correctly with the capabilities() function. Note that X11 = TRUE is required for graphical output, and requires X11 forwarding over SSH.

Now you’re ready to install r-basejump.

conda install -c bioconda r-basejump

References

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