package named "sir"

[awakumaya]

Hi,
Could you tell me how to get package named "sir" in some notebooks of scRNA-Seq-invivo/analysis_pipeline directory.
I guess that the sir package means sir directory in the scRNA-Seq-invivo/analysis_pipeline directory. Is that true? If it's true, how do I set up the directory as a R package?

[fheigwer]

The directory you describe does indeed contain an R package that can be installed and contains helper code to support scRNA-Seq analysis. It is maintained by @jan-glx

[jan-glx]

That's right, the helper package sir is contained in the directory scRNA-Seq-invivo/analysis_pipeline/sir.

You can install it from your local clone of the repository by running make install within the analysis_pipeline directory,

or, as revealed by the makefile, by running remotes::install_local("sir") within R while having analysis_pipeline as working directory.

You can also install it directly from github using: remotes::install_github("boutroslab/Supp_Funk_2021", subdir = "scRNA-Seq-invivo/analysis_pipeline/sir") ( This may take a minute to download before installation starts since this repo is quite big)

Please kindly let us know if you have any other issues running our code!