This repository details the pipeline used to deconvolute bulk RNA-seq data using scRNA-seq as reference. The aim of this project is to evaluate the feasibility of applying reference-based bulk tissue deconvolution algorithms to heart tissues.
The general project workflow is as follows: Pre-processing of scRNA-seq data was first performed before guided clustering was carried out in Seurat. Bulk tissue deconvolution using the Bisque reference-based decomposition model was performed using 4 inputs: 1) unnormalised bulk RNA-seq, 2) unnormalised scRNA-seq, 3) cell-type proportions from guided clustering and 4) DEGs from guided clustering. Estimated cell-type proportions from deconvolution results were compared with those from guided clustering to evaluate the accuracy of cell-type proportions from Bisque.
Project overview:
