inst/scripts/1.0.0/make-tenx-2.1.0-pbmc4k.R

In LTLA/DropletTestFiles: Test Files for Single-Cell Droplet Utilities

base.url <- "https://cf.10xgenomics.com/samples/cell-exp/2.1.0/pbmc4k"

files <- read.csv(text="name,description,output
pbmc4k_raw_gene_bc_matrices.tar.gz,raw count matrix,raw.tar.gz
pbmc4k_filtered_gene_bc_matrices.tar.gz,filtered count matrix,filtered.tar.gz
pbmc4k_raw_gene_bc_matrices_h5.h5,raw HDF5 matrix,raw.h5
pbmc4k_molecule_info.h5,molecule information file,mol_info.h5")

prefix <- "tenx-2.1.0-pbmc4k"
version <- "1.0.0"

out <- DropletTestFiles:::download10xData(
    files=files,
    base=base.url,
    prefix=prefix,
    version=version,
    short="10X PBMC 4k",
    long="10X Genomics single-cell RNA-seq for 4K PBMCs from a healthy donor (3' v2 chemistry, CellRanger 2.1.0)",
    BiocVersion="3.12",
    Genome="hg38",
    SourceUrl="https://support.10xgenomics.com/single-cell-gene-expression/datasets/2.1.0/pbmc4k"
)

write.csv(out, row.names=FALSE,
    file=file.path("../../extdata", version, paste0("metadata-", prefix, ".csv")))