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
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)
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
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