README.md

Causal-inference-in-IBD

Gao, Sheng, et al. "IBD Subtype-Regulators IFNG and GBP5 Identified by Causal Inference Drive More Intense Innate Immunity and Inflammatory Responses in CD Than Those in UC." Frontiers in Pharmacology 13 (2022).

Usage

python dowhy_IBD.py

Input

1. A prior graph edges file: it can be downloaded such as .kgml or .gml files in KEGG website, then convert it into a dataframe (see in example files).
2. A dataframe with gene expressions: row as sample, col as geneID (the last col as condition)

Output

CI_result file with causal inference estimation value of each gene.