Specialised Environments

Page tree

What packages are installed?

The module NCI-bio-R/2021.07 provides a number of popular R packages such as tidyverse as well as a bioconductor environment (version 3.12). These are compiled to work with the R/4.0.0 modules available on gadi and the OOD environment. The main packages are:

From bioconductor:

  • AnnotationDbi
  • AnnotationHub
  • ChIPpeakAnno
  • DESeq2
  • ExperimentHub
  • Genomic Features
  • GenomicAlignments
  • GenomicFeatures
  • IRdisplay
  • IRkernel
  • Rsubread
  • SRAdb
  • ShortRead
  • SingleCellExperiment
  • VariantAnnotation
  • VariantTools
  • biomaRt
  • devtools
  • ensemblVEP
  • ensembldb
  • ggbio
  • h5vc
  • karyoploteR
  • pbdZMQ
  • remote
  • reticulate
  • scRNAseq
  • scran
  • snpStats
  • tidyverse
  • uuid

From CRAN:

  • plotly
  • tidymodels

Extending the environment by adding new packages

Packages can be installed in your own environment and accessed within R when using the packages within the module.

On OOD

On OOD use the .libPaths() command to alter the library search path:

.libPaths( c( "<path-to-R-packages>", .libPaths()))

On gadi

On gadi, use the R_LIBS_USER environment variable or alter the library path within a R script or interactive session using the same .libPaths command as OOD.

  • No labels