AcidSingleCell

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

Installation

This is an R package.

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

Conda method

Configure Conda to use the Bioconda channels.

# Don't install recipe into base environment.
name='r-acidsinglecell'
conda create --name="$name" "$name"
conda activate "$name"
R

Docker method

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