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

scRNAseq-package

R Documentation

Collection of Public Single-Cell RNA-Seq Datasets

Description

Gene-level counts for a collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

Details

This package contains a collection of three publicly available single-cell RNA-seq datasets.

The dataset fluidigm contains 65 cells from Pollen et al. (2014), each sequenced at high and low coverage.

The dataset th2 contains 96 T helper cells from Mahata et al. (2014).

The dataset allen contains 379 cells from the mouse visual cortex. This is a subset of the data published in Tasic et al. (2016).

See the package vignette for details on the pre-processing of the data.

Author(s)

Davide Risso [aut, cph], Michael Cole [aut], Aaron Lun [ctb, cre], Alan O'Callaghan [ctb], Jens Preussner [ctb], Charlotte Soneson [ctb], Stephany Orjuela [ctb], Daniel Bunis [ctb], Milan Malfait [ctb]

Maintainer: Aaron Lun <infinite.monkeys.with.keyboards@gmail.com>

References

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).

LTLA/scRNAseq documentation built on June 28, 2024, 7:31 p.m.