Updates 2026

Since Python2 is discontinued, we are currently migrating CT-FM to a newer version of ldsc which works with Python3. For now, we integrated the ldsc version proposed by Stephen Dorn: https://github.com/svdorn/ldsc-2.0.1

We are now providing a summary of codes to generate the results from our preprint - https://www.medrxiv.org/content/10.1101/2024.05.17.24307556v2 - see here

Our CT-FM paper is now published in Cell Genomics : https://www.cell.com/cell-genomics/fulltext/S2666-979X(26)00187-4

CT-FM and CT-FM-SNP - Cell Type Fine-Mapping

CT-FM and CT-FM-SNP are statistical genetics methods to identify causal cell types underlying diseases/complex traits and particular candidate SNPs, respectively. We leverage cell type specific candidate cis-regulatory elements (cCREs) together with GWAS summary statistics while accounting for co-regulation of cis-regulatory effects across diverse cell types.

Contacts:
Artem Kim artemkim@usc.edu
Steven Gazal gazal@usc.edu

Installation

Pre-requisites

Make sure to have anaconda/conda and mamba installed in your…