Toolkit for single-cell RNA-seq analysis that extends the functionality of SingleCellExperiment.

Installation

Requirements: R >= 4.0, Bioconductor >= 3.12.

R method

if (!requireNamespace("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}
install.packages(
    pkgs = "AcidSingleCell",
    repos = c(
        "https://r.acidgenomics.com",
        BiocManager::repositories()
    )
)

Docker method

image="acidgenomics/r-acidsinglecell"
workdir="/mnt/work"
docker pull "$image"
docker run -it \
    --volume="${PWD}:${workdir}" \
    --workdir="$workdir" \
    "$image" \
    R