lungSS2mca1: Lung scRNA-Seq atlas SmartSeq2 from Mouse Cell Atlas-1

In aet21/EpiSCORE: Epigenetic cell-type deconvolution with Single-Cell Omic References

Lung scRNA-Seq atlas SmartSeq2 from Mouse Cell Atlas-1

Description

The data has been log2-normalized with a pseudocount of 1, so that zeroes correspond to zero mapped reads. The integer cell-type index vector annotates each cell/column to a cell-type, with 1,2,3 and 4 indicating epithelial, endothelial, fibroblast and immune-cell, respectively. An additional vector specifies the cell-types.

Usage

data(lungSS2mca1)

Format

Contains the normalized SmartSeq2 lung atlas from MCA1 with rows labeling 15845 genes and columns labeling 1641 cells, an integer cell-type index vector, and the names of the cell-types.

Details

Upon loading the data object, we find the following:

• lungSS2mca1.m: the scRNA-Seq data matrix

• celltypeSS2.idx: the integer cell-annotation index vector

• celltypeSS2.v: the names of unique cell-types

References

Teschendorff AE, Zhu T, Breeze CE, Beck S. Cell-type deconvolution of bulk tissue DNA methylomes from single-cell RNA-Seq data Genome Biol.2020

aet21/EpiSCORE documentation built on June 26, 2022, 5:50 p.m.