-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Added scripts for the Ernst dataset.
- Loading branch information
Showing
2 changed files
with
19 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,5 @@ | ||
# 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. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,14 @@ | ||
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) |