TRef: Reference profiles obtained from single cell data of tumor...

In GfellerLab/EPIC: Estimate the Proportion of Immune and Cancer cells

Reference profiles obtained from single cell data of tumor infiltrating cells.

Description

A dataset containing the reference profiles obtained from various tumor infiltrating non-malignant cell types: B cells, cancer-associated fibroblasts, CD4 T cells, CD8 T cells, endothelial cells, Macrophages and NK cells.

Usage

TRef

Format

A list of 3 elements:

$refProfiles, $refProfiles.var

Matrices (nGenes x nRefCells) of the gene expression (in TPM counts) from the reference cells and the variability of this gene expression for each gene and each cell type

$sigGenes

A list of signature genes used to deconvolve the cell proportions

Details

These were obtained from single-cell RNA-seq data from 9 donors from the publication of Tirosh et al., 2016, Science. The samples come from melanoma tumors (extracted from primary tumors and non-lymphoid tissue metastases). The classification for each sample with respect to each cell type is the one given by Tirosh et al., except for the CD4 T cells and CD8 T cells, that were identified from the T cells based on the expression of CD4, CD8A and CD8B as described in Racle et al., 2017, eLife.

Source

http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056

GfellerLab/EPIC documentation built on July 22, 2023, 2:06 a.m.