mgibio/r-singlecell repository overview

⁠docker-single-cell

Basic docker image for single-cell analyses - combines a lot of the tools that are handy for exploring data on a ubuntu base image.

⁠Notes:

• R 3.5 and some basic packages are installed (Seurat, DropletUtils). For convenience, it can be useful to set up a specific folder in which to keep your own library installs for testing. This will keep them persistent across sessions. Add something like this to your .Rprofile:

  devlib <- paste('/gscuser/cmiller/usr/lib/R',paste(R.version$major,R.version$minor,sep="."),sep="")
  if (!file.exists(devlib))
  dir.create(devlib)
  x <- .libPaths()
  .libPaths(c(devlib,x))
  rm(x,devlib)```
  

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This is great for quickly prototyping, but don't forget that if you're sharing code with others, you'll need to create a new container with the proper libraries installed so they can also use it!