I am trying to analyze the scRNAseq data from this study. In their Method section they write:
The accession number for the RNA and DNaseq data reported in this paper is GEO: GSE116237.
When I go ahead and try to pull this data in R using
GEOquery, I am faced with a data frame with no features (i.e. no genes). The following code
library("GEOquery") gse <- getGEO("GSE116237") eset1 <- gse[] eset2 <- gse[] print(dim(eset1)) print(dim(eset2))
Features Samples 0 184 Features Samples 0 681
I also didn't manage to download the data manually; I get an error message when trying to unzip the
.zip files or get redirected to SRA Run Selector from which I also didn't manage to figure out how to download stuff.
Am I missing something or are these files simply corrupted? The paper is published in Cell, so I would assume this data is, to some extend, legit...