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

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

Downloading the count data

We obtain a single-cell RNA sequencing dataset of human pancreas from @grun2016denovo. A count matrix for endogenous genes and spike-ins is provided from the Gene Expression Omnibus using accession code GSE81076. We download it using r Biocpkg("BiocFileCache") to cache the results:

library(BiocFileCache)
bfc <- BiocFileCache("raw_data", ask=FALSE)
grun.fname <- bfcrpath(bfc, file.path("ftp://ftp.ncbi.nlm.nih.gov/geo/series",
    "GSE81nnn/GSE81076/suppl/GSE81076%5FD2%5F3%5F7%5F10%5F17%2Etxt%2Egz"))

We read the table into memory as a sparse matrix.

library(scater)
counts <- readSparseCounts(grun.fname, quote="\"")
dim(counts)

Saving to file

We save all of the components to file for upload to r Biocpkg("ExperimentHub").

path <- file.path("scRNAseq", "grun-pancreas", "2.0.0")
dir.create(path, showWarnings=FALSE, recursive=TRUE)
saveRDS(counts, file=file.path(path, "counts.rds"))

Session information

sessionInfo()

References

drisso/scRNAseq documentation built on Feb. 16, 2021, 1:18 a.m.