requiredSoftware.md

R packages - on HPC

• BiocManager
• hdf5r
• Seurat
• Signac
• SingleCellExperiment
  • BiocManager::install("SingleCellExperiment")
• tidyverse
• qs
• nichenetr
  • https://github.com/saeyslab/nichenetr
• rrrSingleCellUtils
  • https://github.com/kidcancerlab/rrrSingleCellUtils
• GenomicFeatures
  • BiocManager::install("GenomicFeatures")
• EnsDb.Mmusculus.v79
  • BiocManager::install("EnsDb.Mmusculus.v79")
• SingleR
  • BiocManager::install("SingleR")
• celldex
  • BiocManager::install("celldex")

R packages - on local machine

• Seurat
• tidyverse
• qs

HPC modules

• GCC/9.3.0
• OpenMPI/4.0.3
• R/4.2.2'
• rstudio/1.4.1717
• HDF5