diff --git a/bacher-tcell/README.md b/bacher-tcell/README.md new file mode 100644 index 0000000..71e7187 --- /dev/null +++ b/bacher-tcell/README.md @@ -0,0 +1,4 @@ +# Bacher T cell single-cell RNA-seq dataset + +This takes the T cell dataset from [Bacher _et al._ (2020)](https://pubmed.ncbi.nlm.nih.gov/33296686/) and provides it in the 10X HDF5 and MatrixMarket formats. +Run `generate.R` to construct the files. diff --git a/bacher-tcell/generate.R b/bacher-tcell/generate.R new file mode 100644 index 0000000..43d61b8 --- /dev/null +++ b/bacher-tcell/generate.R @@ -0,0 +1,12 @@ +library(scRNAseq) +sce <- BacherTCellData() + +# Saving in version 3 of the 10x format. +library(DropletUtils) +write10xCounts("mtx", assay(sce), version="3", overwrite=TRUE) + +# Saving in version 3 of the 10x format. +source("../_scripts/compact10x.R") +name <- "tenx.h5" +unlink(name) +compact10x(name, assay(sce), rownames(sce), rownames(sce))