Added scripts for the Bacher dataset.

kanaverse · Jan 25, 2022 · e547526 · e547526
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diff --git a/bacher-tcell/README.md b/bacher-tcell/README.md
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+# 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
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+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))