This package contains a collection of three publicly available single-cell RNA-seq datasets. The data were downloaded from NCBI's SRA or from EBI's ArrayExpress (see below for Accession numbers) and pre-processed with a standardized pipeline (see vignette). For each dataset, the package provides gene-level read counts obtained from Tophat + featureCounts, gene-level FPKMs obtained from Cufflinks, and gene-level read counts and TPMs from RSEM.
The dataset fluidigm contains 65 cells from Pollen et al. (2014), each sequenced at high and low coverage (SRA: SRP041736).
The dataset th2 contains 96 T helper cells from Mahata et al. (2014) (ArrayExpress: E-MTAB-2512).
The dataset allen contains 379 cells from the mouse visual cortex. This is a subset of the data published in Tasic et al. (2016) (SRA: SRP061902).
You can download the latest release here. Once dowloaded, type in R
install.packages("scRNAseq_0.99.0.tar.gz", repos=NULL)
to install the package, where scRNAseq_0.99.0.tar.gz is the name of the file downloaded (note that the name could change reflecting the release of a new version of the package).
Note that this package depends on the Bioconductor package SummarizedExperiment, which can be installed in R by typing
source("https://bioconductor.org/biocLite.R")
biocLite("SummarizedExperiment")
Pollen, Nowakowski, Shuga, Wang, Leyrat, Lui, Li, Szpankowski, Fowler, Chen, Ramalingam, Sun, Thu, Norris, Lebofsky, Toppani, Kemp II, Wong, Clerkson, Jones, Wu, Knutsson, Alvarado, Wang, Weaver, May, Jones, Unger, Kriegstein, West. Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex. Nature Biotechnology, 32, 1053-1058 (2014).
Mahata, Zhang, Kolodziejczyk, Proserpio, Haim-Vilmovsky, Taylor, Hebenstreit, Dingler, Moignard, Gottgens, Arlt, McKenzie, Teichmann. Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis. Cell Reports, 7(4): 1130–1142 (2014).
Tasic, Menon, Nguyen, Kim, Jarsky, Yao, Levi, Gray, Sorensen, Dolbeare, Bertagnolli, Goldy, Shapovalova, Parry, Lee, Smith, Bernard, Madisen, Sunkin, Hawrylycz, Koch, Zeng. Adult mouse cortical cell taxonomy revealed by single cell transcriptomics. Nature Neuroscience, 19, 335–346 (2016).
The data were downloaded from NCBI's SRA or from EBI's ArrayExpress. See the following disclaimers for copyright / license policies.