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).
To install the package from Github,
library(devtools)
install_github("kkdey/singlecellRNAseqData")
Load the package
library(singlecellRNAseqData)
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.
The singlecellRNAseqData package is distributed under [GPL - General Public License (>= 2)]
For any queries, contact kkdey@uchicago.edu
- Rickard Sandberg