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Base functions for bioinformatics and R package development.
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README.md

basejump

Travis CI build status AppVeyor CI build status Anaconda cloud version Repo status: active

Base functions for bioinformatics and R package development.

Installation

Bioconductor method

We recommend installing the package with BiocManager.

if (!require("BiocManager")) {
    install.packages("BiocManager")
}
BiocManager::install("remotes")
BiocManager::install("acidgenomics/basejump")

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

References

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

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