README

Singularity image with pre-installed libraries for running gene ontology analysis in R.

The included libraries:

Gene and genome annotation

• clusterProfiler - enrichment tool for interpreting omics data
• ReactomePA - reactome pathway analysis
• biomaRt
• org.Mm.eg.db - Genome wide annotation for Mouse
• org.Hs.eg.db - Genome wide annotation for Human

Utility

• gtools
• scales
• openxlsx

Build

Use the definition file to build locally:

apptainer build gene_ontology.sif gene_ontology.def

Deploy

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

apptainer pull library://andreyhgl/singularity-r/gene-ontology: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(scales)
  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/gene-ontology:latest script-file.R