Skip to content

Latest commit

 

History

History
34 lines (27 loc) · 2.24 KB

README.md

File metadata and controls

34 lines (27 loc) · 2.24 KB

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:

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