TFXcan

TFXcan (transcription factor binding prediction and correlation with complex traits).

Date

Wednesday, June 18 2025

Author

Temi

Description

In addtion, we provide access to the following pipelines to generate the data used in the paper:

1. To train DL-based predictors of TF binding, use this pipeline: https://github.com/hakyimlab/TFPred-snakemake
2. To run TFXcan, i.e. to find transcription factors that are associated with a trait, use this pipeline: https://github.com/hakyimlab/TFXcan-snakemake

Brief description of scripts and folders

• reproduceData: contains step-by-step instructions to run scripts that reproduce the main results and data in the TFXcan paper. THIS IS NOT AN ANALYSIS SCRIPT. It is written in Quarto and can be rendered to HTML or PDF, or run interactively in RStudio.
• src: contains standalone bash, r or python scripts. Used in the reproduceData notebook.
• software: contains software used such as liftover, e.t.c.
• metadata: contains some files and data used to analyse the results.
• recreateAnalysis: contains scripts to reproduce the analysis, figures, supplementary figures, data and results in the TFXcan paper.
• misc: contains some random scripts and files [to be deleted later].