MultiRD: Multi-Robust Cell-type Deconvolution of Bulk RNA Sequencing Data via Integrating Information from Single-cell Reference and External Expression Data

MultiRD unifies multiple deconvolution schemes to infer cell type proportions from the target bulk RNA-seq data. Three unique features are embraced in this algorithm: first, MultiRD is able to incorporate extra biological information from external data sources enables (e.g., scRNA_seq and other bulk RNA_seq data from independent studies); second, MultiRD calibrates the reference-free algorithm by taking into account the proportion estimates from a reference-based approach; third, MultiRD is robust to incorrect information from any of the provided data sources.

Installation

You can install the released version of MultiRD with:

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

#install the MultiRD package
devtools::install_github("chencxxy28/MultiRD")

#load
library(MultiRD)

If Biobase package is not available, please install it first before installation of MultiRD

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("Biobase")

Vignettes

Please visit Tutorial.