README

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

The included libraries:

Visualisation

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

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

• dplyr

• reshape2 (included with other packages)

• Quarto v1.8.27 (to build dashboards with tabsets)

Build

Use the definition file to build locally:

apptainer build RNAseq.sif RNAseq.def

Tip

Use a non-interactive install by adding -y

%post
  apt-get update

  # Install less and qpdf
  apt-get install -y less
  apt-get install -y qpdf

Deploy

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

apptainer pull library://andreyhgl/singularity-r/rnaseq:latest

Tip

If apptainer/singularity is not working, try adding the remote host 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://andreyhgl/singularity-r/rnaseq:latest script-file.R