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")
• biovizBase
  • BiocManager::install("biovizBase")
• org.Hs.eg.db
  • BiocManager::install("org.Hs.eg.db")
• BSgenome.Mmusculus.UCSC.mm10
  • BiocManager::install("BSgenome.Mmusculus.UCSC.mm10")
• qlcMatrix
• JASPAR2020
  • BiocManager::install("JASPAR2020")
• TFBSTools
  • BiocManager::install("TFBSTools")
• motifmatchr
  • BiocManager::install("motifmatchr")

R packages - on local machine

• Seurat
• tidyverse
• qs

Programs on local machine

• R
• Rtools (windows only)
• RStudio
• git

HPC modules

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