r-scrnaseq

r-scrnaseq is a customerized R module based on R/4.1.1 or R/4.2.0 used for scRNAseq analysis.

In the module, we have some packages installed:

BiocManager 1.30.16
CellChat 1.6.1
ProjecTILs 3.0
Seurat 4.1.0
SeuratObject 4.0.4
SeuratWrappers 0.3.0
monocle3 1.0.0
SnapATAC 1.0.0
SingleCellExperiment 1.14.1, 1.16.0
scDblFinder 1.8.0
SingleR 1.8.1
scCATCH 3.0
scMappR 1.0.7
rliger 1.0.0
schex 1.8.0
CoGAPS 3.14.0
celldex 1.4.0
dittoSeq 1.6.0
DropletUtils 1.14.2
miQC 1.2.0
Nebulosa 1.4.0
tricycle 1.2.0
pheatmap 1.0.12
limma 3.48.3, 3.50.0
tibble 3.1.5
tidyr 1.1.4
readr 2.0.2
readxl 1.3.1
purrr 0.3.4
dplyr 1.0.7
stringr 1.4.0
forcats 0.5.1
ggplot2 3.3.5
openxlsx 4.2.5

Link to section 'Versions' of 'r-scrnaseq' Versions

4.1.1-1
4.1.1-1-rstudio
4.2.0
4.2.0-rstudio
r-scrnaseq/4.2.3-rstudio

Link to section 'Commands' of 'r-scrnaseq' Commands

R
Rscript
rstudio (only for the rstudio version)

Link to section 'Module' of 'r-scrnaseq' Module

You can load the modules by:

module load biocontainers  
module load r-scrnaseq
# or module load r-scrnaseq/4.2.0
# If you want to use Rstudio, load the rstudio version
module load r-scrnaseq/4.1.1-1-rstudio 
# or module load r-scrnaseq/4.2.0-rstudio

Install packages

Users can also install packages they need. The installed location depends on the setting in your ~/.Rprofile.
Detailed guide about installing R packages can be found here: https://www.rcac.purdue.edu/knowledge/bell/run/examples/apps/r/package.

Link to section 'Interactive job' of 'r-scrnaseq' Interactive job

To run interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers r-scrnaseq/4.2.0 # or r-scrnaseq/4.2.0-rstudio 
(base) UserID@bell-a008:~ $ R

R version 4.2.0 (2022-04-22) -- "Vigorous Calisthenics"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.


> library(Seurat)
> library(monocle3)

Link to section 'Batch job' of 'r-scrnaseq' Batch job

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To submit a sbatch job on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name 
#SBATCH -t 10:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH --job-name=r_scRNAseq
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers r-scrnaseq

Rscript scRNAseq.R

Helpful?