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Seurat-Integrate

R package gathering a set of wrappers to apply various integration methods to Seurat objects and rate integration obtained with such methods

Installation

1) Remotely from github with R

Install SeuratIntegrate from github directly:

install.packages(c("remotes", "BiocManager"))
remotes::install_github("cbib/Seurat-Integrate", dependancies = NA, repos = BiocManager::repositories())

If you prefer, or if it does not work, you can use the alternative way described below.

2) From a local copy using the remotes R package

The installation process encompasses two steps, namely:

  • Clone or download the repository or the latest release
  • Install the package

First off, go to some/path/to/download/the/repository. Then, clone or download the repository or a release.

# Example: clone
git clone git@github.com:cbib/Seurat-Integrate.git

Depending on what you chose to download, you can either obtain the source code in a Seurat-Integrate/ folder or a compressed version ending with .targ.gz. Regardless, you can use the command below:

install.packages(c("remotes", "BiocManager"))
path <- 'Seurat-Integrate/'   # or SeuratIntegrate_X.X.X.tar.gz (X.X.X being the version)
remotes::install_local(path = path, dependencies = NA, repos = BiocManager::repositories())

Done ! Open a R session and try it out !