From 0d987ab3db4180dbe629ff7e97f2c2db812b167c Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Mon, 24 Jan 2022 23:24:51 -0800
Subject: [PATCH] Added scripts for the Zilionis lung dataset.

---
 zilionis-lung/README.md  |  4 ++++
 zilionis-lung/generate.R | 12 ++++++++++++
 2 files changed, 16 insertions(+)
 create mode 100644 zilionis-lung/README.md
 create mode 100644 zilionis-lung/generate.R

diff --git a/zilionis-lung/README.md b/zilionis-lung/README.md
new file mode 100644
index 0000000..3eeabd9
--- /dev/null
+++ b/zilionis-lung/README.md
@@ -0,0 +1,4 @@
+# Zilionis lung single-cell RNA-seq dataset
+
+This takes the lung dataset from [Bacher _et al._ (2020)](https://pubmed.ncbi.nlm.nih.gov/30979687/) and provides it in the 10X HDF5 and MatrixMarket formats.
+Run `generate.R` to construct the files.
diff --git a/zilionis-lung/generate.R b/zilionis-lung/generate.R
new file mode 100644
index 0000000..72043dc
--- /dev/null
+++ b/zilionis-lung/generate.R
@@ -0,0 +1,12 @@
+library(scRNAseq)
+sce <- ZilionisLungData()
+
+# 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))