Bioconductor data package for hosting single cell RNA-seq data
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DESCRIPTION
NAMESPACE
NEWS
README.md
singlecellRNAseqData.Rproj

README.md

singlecellRNAseqData

Bioconductor data package for hosting single cell RNA-seq data as ExpressionSet objects. The datasets include Mouse spleen single cell data due to Jaitin et al (2014), Mouse embryonic stem cell data across different stages of embryo development due to Deng et al (2014) and Mouse single cell data from cortex and hippocampus due to Zeisel et al (2015).

Installation

To install the package from Github,

library(devtools)
install_github("kkdey/singlecellRNAseqData")

Load the package

library(singlecellRNAseqData)

Data Processing

We present the steps to load the expression data and sample and feature metadata using the example of the Deng et al (2014) data.

data("MouseDengESC")

RNA-seq counts or expression data

exprs(MouseDengESC)

The sample metadata

pData(MouseDengESC)

The feature metadata

featureData(MouseDengESC)

To load the other two datasets due to Jaitin et al (2014) and Zeisel et al (2015).

data("MouseJaitinSpleen")
data("MouseZeiselBrain")

The processing steps for expression data, sample and feature metadata extraction for these two datasets is similar as above.

Licenses

The singlecellRNAseqData package is distributed under [GPL - General Public License (>= 2)]

Contact

For any queries, contact kkdey@uchicago.edu

Acknowledgements

  • Rickard Sandberg