This repository has been moved!

This repository has been moved to https://github.com/andreyhgl/containeR-RNAseq

// Andrey

README

Singularity image with pre-installed libraries for running bulk RNA-seq analysis in R.

The included libraries:

Visualisation

• ggplot2
• ggrepel
• ggsignif
• cowplot
• RColorBrewer
• patchwork
• ComplexHeatmap

Differential gene expression analysis

• edgeR
• DESeq2

Gene and genome annotation

• clusterProfiler
• ReactomePA
• biomaRt
• org.Mm.eg.db
• org.Hs.eg.db
• tximport

Utility

• gtools
• tools
• scales
• data.table
• forcats
• openxlsx
• readr

Build

Use the definition file to build locally:

apptainer build bulk-RNAseq.sif bulk-RNAseq.def

Deploy

Pre-build image can be downloaded from the Cloud Library:

apptainer pull library://flerpan01/singularity-r/bulk-rnaseq:latest

Note, with apptainer the remote singularity host might need to be added manually

# list the remote URI
singuliarty remote list

# add singularity cloud URI
apptainer remote add --no-login SylabsCloud cloud.sycloud.io

Execute scripts

In order to fully utilise the singularity image make sure a shebang is included in the script file #!/usr/bin/env Rscript.

#!/usr/bin/env Rscript

suppressPackageStartupMessages({
  library(edgeR)
  library(gtools)
})

...

Also make the script file executable.

chmod +x script-file.R

The singularity image expects a script file on exec.

apptainer exec library://flerpan01/singularity-r/bulk-rnaseq:latest script-file.R