See Also

Related Projects

LDGM Repository

Main LDGM repository with MATLAB API:

• https://github.com/awohns/ldgm

graphREML (MATLAB)

Original graphREML implementation in MATLAB:

• https://github.com/huilisabrina/graphREML

We recommend using the Python implementation in this repository, which is much faster.

LD Score Regression

Reference implementation of LD score regression:

• https://github.com/bulik/ldsc

LDGM-VCF (bcftools)

Giulio Genovese's bcftools plugin with LDGM-VCF file format specification and C implementation:

• https://github.com/freeseek/score

SuiteSparse

Sparse matrix operations used by graphld:

• https://github.com/DrTimothyAldenDavis/SuiteSparse

Citations

If you use this software, please cite:

graphREML

Hui Li, Tushar Kamath, Rahul Mazumder, Xihong Lin, & Luke J. O'Connor (2024). Improved heritability partitioning and enrichment analyses using summary statistics with graphREML. medRxiv, 2024-11. DOI: 10.1101/2024.11.04.24316716

LDGM

Pouria Salehi Nowbandegani, Anthony Wilder Wohns, Jenna L. Ballard, Eric S. Lander, Alex Bloemendal, Benjamin M. Neale, and Luke J. O'Connor (2023). Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies. Nat Genet. DOI: 10.1038/s41588-023-01487-8