Base functions for bioinformatics and R package development.
Bioconductor method
We recommend installing the package with BiocManager.
if (!require("BiocManager")) {
install.packages("BiocManager")
}
BiocManager::install("remotes")
BiocManager::install("steinbaugh/basejump", ref = "v0.7.2")
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 method
Configure conda to use the bioconda channels.
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
To avoid version issues, your .condarc
file should only contain the following channels, in this order:
channels:
- conda-forge
- bioconda
- 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=0.7.2
The papers and software cited in our workflows are available as a shared library on Paperpile.