SECRET

Semi-reference based cell type deconvolution

SECRET, a reference-based approach, leverages the cell type-specific gene expression profiles obtained from single-cell RNA-Seq to effectively estimate cell type proportions in bulk data, particularly in instances where the bulk data contains cell types that are not present in the reference dataset.

Installation

Dependencies

• R version >= 4.0.0.
• R packages: Biobase, tidyverse, NOISeq, alabama

# install devtools if necessary
install.packages('devtools')

# install the SECRET package
devtools::install_github('YyLu5/SECRET')

# load
library(SECRET)

• For an example how to use SECRET
• Example datasets are in vignettes folder