In wguo-research/scCancer: A package for automated processing of single cell RNA-seq data in cancer

r h.i.r h.ii Cancer micro-environmental cell types annotation

In order to annotate major microenvironment cell types, including endothelial cells, fibroblast, and immune cells (CD4+ T cells, CD8+ T cells, B cells, nature killer cells, and myeloid cells), we use a one-class logistic regression (OCLR) model to perform prediction. The predicted cell type results can be found in the column Cell.Type of the table file cellAnnotation.txt. And the correlation coefficients with cell type templates are in columns *.corr.

Here is the scatter plot colored by predicted cell types.

results$cellType.plot$p.type

(Hi-res image: view)

Here is a bar plot showing the relationship between cell cluster and cell type annotation.

results$cellType.plot$p.bar

(Hi-res image: view)

h.ii <- h.ii + 1

wguo-research/scCancer documentation built on May 26, 2024, 9:12 p.m.