README

This repository holds a singularity / apptainer image with pre-installed R libraries for analysing DNA methylation generated from RRBS, BS-seq and EM-seq. Genome annotation libraries included for both human and mouse. Differential methylation calculation packages include are edgeR and methylKit.

---

Libraries list

Visualisation

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

Differential methylation analysis

• edgeR
• methylKit

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 containeR-methylome.sif containeR-methylome.def

Deploy

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

apptainer pull library://andreyhgl/singularity-r/methylome

Note

With apptainer and on HPCs the remote singularity host might need to be added manually

# list the remote URI
apptainer 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(methylKit)
	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/methylome script.R