Single Cell

single cell RNAseq

Shared installation in O2

There is a Rlib shared installation in O2 with seurat and zinbvawe and tidyverse packages.

To use it, load:

module load module load gcc/6.2.0 R/3.4.1 gsl

Add this to ~/.Renviron

R_LIBS_USER=/n/data1/cores/bcbio/R/library/3.4-bioc-release/library
R_MAX_NUM_DLLS=150

Then just type R or use Rscript.

Docker container with bcbioSingleCell

There is a docker container with the last version of R and Seurat installed and kind of updated bcbioSingleCell package.

To set up the Docker container to run the single-cell RNA-Seq analysis using bcbioSingleCell and Seurat, we need to perform a few steps.

NOTE: There are nice tutorials online to help understand the basics of Docker, including Docker for beginners and Titus' materials.

To set up Docker on a local computer, install the Docker application, then run the docker pull command using the r3.5-bsc0.1.5 tag available from lpantano/bcbiosinglecell(available tags can be found here):

docker pull lpantano/bcbiosinglecell:r3.5-bsc0.1.5

After pulling the docker image, run the container as detailed at https://hub.docker.com/r/lpantano/bcbiosinglecell/. This site also has explanations on how to install/update packages when you have it running in your local computer.