2. Prerequisites and required machine configuration

Prerequisites

The course is intended for those who have basic familiarity with Unix and the R scripting language.

  • If a refresher is needed for Unix command line (hopefully not), please go over this tutorial and its companion cheatsheet.
  • Getting down to basics: an introduction to the fundamentals of R (courtesy of Mark Ravinet).
  • Gentle introduction to R/Biocondutor: here
  • For a full in-depth guide of Bioconductor ecosystem: read the comprehensive R/Bioconductor book from Kasper D. Hansen available under the CC BY-NC-SA 4.0 license [PDF]

Local configuration

  • Install R and other important softwares
conda create --name scatac
conda activate scatac
conda install -c conda-forge -c bioconda \
    r-base r-essentials r-devtools r-tidyverse r-biocmanager r-polyclip r-rcpparmadillo \
    trim-galore bowtie2 samtools deeptools meme macs2 igv sinto yapc htseq subread ucsc-bedgraphtobigwig bedtools
conda install -c anaconda hdf5
  • The following R packages have also been installed (along with their many dependencies, of course!):
Rscript -e "
## CRAN packages
install.packages('vroom', repos = 'https://cran.irsn.fr')
install.packages('hdf5r', dependencies=TRUE, repos = 'https://cran.irsn.fr')
install.packages('umap', repos = 'https://cran.irsn.fr')
install.packages('corrplot', repos = 'https://cran.irsn.fr')
install.packages('gam', repos = 'https://cran.irsn.fr')
install.packages('ggbeeswarm', repos = 'https://cran.irsn.fr')
install.packages('ggthemes', repos = 'https://cran.irsn.fr')
install.packages('Matrix', repos = 'https://cran.irsn.fr')
install.packages('rgl', dependencies=TRUE, repos = 'https://cran.irsn.fr')
install.packages('Signac', repos = 'https://cran.irsn.fr')
install.packages('Seurat', repos = 'https://cran.irsn.fr')
install.packages('BiocManager', repos = 'https://cran.irsn.fr')

## Bioconductor Packages
BiocManager::install('scRNAseq', update = FALSE)
BiocManager::install('SingleR', update = FALSE)
BiocManager::install('SingleCellExperiment', update = FALSE)
BiocManager::install('scran', update = FALSE)
BiocManager::install('scater', update = FALSE)
BiocManager::install('DESeq2', update = FALSE)
BiocManager::install('chromVAR', update = FALSE)
BiocManager::install('pheatmap', update = FALSE)
BiocManager::install('JASPAR2020', update = FALSE)
BiocManager::install('motifmatchr', update = FALSE)
BiocManager::install('AnnotationHub', update = FALSE)
BiocManager::install('plyranges', update = FALSE)
BiocManager::install('VplotR', update = FALSE)
BiocManager::install('annotatr', update = FALSE)
BiocManager::install('rtracklayer', update = FALSE)
BiocManager::install('biovizBase', update = FALSE)
BiocManager::install('gprofiler2', update = FALSE)
BiocManager::install('DOSE', update = FALSE)
BiocManager::install('clusterProfiler', update = FALSE)
BiocManager::install('EnsDb.Mmusculus.v79', update = FALSE)
BiocManager::install('EnsDb.Hsapiens.v79', update = FALSE)
BiocManager::install('TxDb.Hsapiens.UCSC.hg38.knownGene', update = FALSE)
BiocManager::install('TxDb.Mmusculus.UCSC.mm10.knownGene', update = FALSE)
BiocManager::install('org.Hs.eg.db', update = FALSE)
BiocManager::install('org.Mm.eg.db', update = FALSE)
BiocManager::install('BSgenome.Celegans.UCSC.ce11', update = FALSE)
"

  • Additional dependencies:

    • cellranger-atac
    • Loupe