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Added scripts for the Ernst dataset.
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LTLA committed Jan 25, 2022
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5 changes: 5 additions & 0 deletions ernst-sperm/README.md
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# Ernst spermatogenesis single-cell RNA-seq dataset

This takes the spermatogenesis dataset from [Ernst _et al._ (2019)](https://www.nature.com/articles/s41467-019-09182-1) and provides it in the 10X HDF5 or Matrix Market formats.
This is a nice dataset, not least because the t-SNE actually looks like a spermatozoa.
Run `generate.R` to construct the files.
14 changes: 14 additions & 0 deletions ernst-sperm/generate.R
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library(scRNAseq)
sce <- ErnstSpermatogenesisData(method="emptyDrops", location=FALSE)
sce <- sce[grep("ENSMUSG", rownames(sce)),]

# 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.
library(HDF5Array)
source("../_scripts/compact10x.R")
name <- "tenx.h5"
unlink(name)
compact10x(name, assay(sce), rownames(sce), rowData(sce)$Symbol)

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