DeconvoBuddies

DeconvoBuddies provides helper functions for cellular deconvolution of bulk RNA-sequencing data, including tools for marker finding with mean ratio, expression plotting, and plotting deconvolution results.

Key Features:

• Mean Ratio Marker Finding: Implements the Mean Ratio method for identifying gene markers for deconvolution.
• Expression Plotting: Generates plots for visualizing gene expression data.
• Deconvolution Result Plotting: Produces plots for visualizing deconvolution algorithm outputs.
• DLPFC Dataset Integration: Incorporates dorsolateral prefrontal cortex datasets for deconvolution analysis.

Scientific Applications:

• Bulk RNA-seq Deconvolution: Estimates cell type composition in heterogeneous tissues using bulk RNA-sequencing data with single cell/nuclei RNA-seq reference data.
• Brain Tissue Analysis: Supports deconvolution of postmortem human brain tissue, specifically dorsolateral prefrontal cortex.
• Deconvolution Algorithm Benchmarking: Facilitates evaluation and comparison of deconvolution algorithms such as Bisque and hspe.

Methodology:

The package implements the Mean Ratio gene marker finding method and provides functions for plotting expression and deconvolution results.