BuDDI Analysis

This repository contains all the code to reproduce the analyses in BuDDI: Bulk Deconvolution with Domain Invariance to predict cell-type-specific perturbations from bulk

Directory Structure

Data for each analysis can be downloaded from figshare under the DOI: 10.6084/m9.figshare.23721336. The expected directory structure is:

• buddi_analysis
  • sc_preprocessing
  • kang_analysis
  • liver_analysis
  • synovium_analysis
  • bayesprism_scripts
  • data (from figshare)
  • results (from figshare)

Contents

A tutorial on how to run a BuDDI analysis is provided in tutorial folder. Data to run the tutorial are also provided in the same folder.

The analysis folders contain the following information:

• sc_preprocessing: single-cell QC scripts and pseudobulk generation code
• kang_analysis: code to generate figures 1-3, supp. fig 1,5,6, supp. table 1
  • This includes the code for CVAE and PCA comparisons in the folder kang_comparators
• liver_analysis: code to generate figure 4, supp. fig 2,3,6, supp. table 2,3
  • This includes the code for CVAE and PCA comparisons in the folder sex_prediction_comparators
• synovium_analysis: code to generate figure 5, supp. fig 7, supp. table 4
• bayesprism_scripts: R and shell scripts to run BayesPrism

Running Analyses

To use these notebooks, it is assumed that you have installed BuDDI in a virtualenv and have activated this venv before running the notebooks. Installation instructions for BuDDI are here: https://github.com/greenelab/buddi/tree/main#buddi