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Using BioConductor with RStudio Package Manager

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RStudio Package Manager doesn't have direct support for BioConductor (yet!). If you are interested in using BioConductor with RStudio Package Manager, please reach out to sales@rstudio.com. In the interim there are two workarounds:
 
1) You can download the BioConductor packages as source tarballs, and then add those tarballs to a local source.
 
Example:
# create a source to hold the BioC packages
rspm create source --name=bioc

# for each package: download and add to the source
wget http://bioconductor.org/packages/release/bioc/src/contrib/BiocGenerics_0.28.0.tar.gz

rspm add --source=bioc --path=BiocGenerics_0.28.0.tar.gz
 

2) BioConductor packages live in Git repositories, so you can also use the built-in Git support to automatically pull in the package sources for either a specific release or the bleeding edge development branch. Do this by using creating a git source for each release, and then adding the desired BioConductor packages to the relevant Git source. 
 
Example:
 
# create a git source for the bleeding edge BioC packages
rspm create source --name=bioc-dev

# add each package to the source
rspm add --source=bioc-dev --git-url=https://git.bioconductor.org/packages/BiocGenerics.git  

# OR create git source for a specific releases of BioC
rspm create source --name=bioc-3.8

# add each package to the source using the release branch
rspm add --source=bioc-3.8 --git-url=https://git.bioconductor.org/packages/BiocGenerics.git  --git-branch=RELEASE_3_8
 
Whether you use Git or a local source,  finish by creating a repository to house the BioC sources and then using install.packages, not BiocManager, to install the packages from RStudio Package Manager. 

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