In LTLA/scRNAseq: Collection of Public Single-Cell RNA-Seq Datasets

library(BiocStyle)
knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)

Obtaining the old version

For reasons I don't understand, the ETL from ExperimentHub to gypsum changed the assay name from normcounts to normalized, even though the GEO entry clearly states that:

Normalized expected counts are provided in GSE64016_H1andFUCCI_normalized_EC.csv.gz

So, okay, we'll change it back. First we clone the old version.

tmp <- "update_20240418"
unlink(tmp, recursive=TRUE) # get rid of any previous directory.
gypsum::cloneVersion("scRNAseq", "leng-esc-2015", "2023-12-18", destination=tmp)

Now we go in and edit the names.

assay.name.path <- file.path(tmp, "assays", "names.json")
assay.names <- jsonlite::fromJSON(assay.name.path, simplifyVector=FALSE)
assay.names

# Replacing the link with the new content; it's important to delete the link
# before doing so, otherwise we would accidentally modify the cache!
unlink(assay.name.path) 
assay.names[[1]][1] <- "normcounts"
write(jsonlite::toJSON(assay.names, auto_unbox=TRUE, pretty=4), file=assay.name.path)

We run some validation to ensure that our modified files are still valid.

library(alabaster.base)
validateObject(tmp)

# Confirming that the assay names changed.
readObject(tmp)

Session information {-}

sessionInfo()

LTLA/scRNAseq documentation built on April 29, 2024, 12:34 p.m.