Cell type decomposition of bulk samples

2023-06-11

scPlant helps estimating the cell type composition of bulk samples using a single cell reference. Cell-type deconvolution was implemented based on the CIBERSORT algorithm. CIBERSORT is an algorithm for estimating the cell type composition of a bulk sample, given a gene expression profile of the sample and a known gene expression profile for each cell type potentially contributing to the sample. Here, we wrap runCIBERSORT function from RNAMagnet R package to decompose bulk RNA-seq samples.

To install RNAMagnet R package, see https://github.com/veltenlab/rnamagnet. Note that MAGIC is an important requirement of RNAMagnet package, and needs to be installed as a python package, see https://github.com/KrishnaswamyLab/MAGIC/tree/master/Rmagic#installation.

library(RNAMagnet)
library(scPlant)

result <- decomposeBulk(SeuratObj, exprs, meta)

Heatmap showing the fraction of cell types in each bulk RNA-seq sample.

fractionHmp(result, meta)