Established: October 14, 2006
Last Update: May 21, 2023
FaST-LMM, which stands for Factored Spectrally Transformed Linear Mixed Models, is a program for performing genome-wide association studies (GWAS) on datasets of all sizes, up to one millions samples.
Learn more about Python FaST-LMM and install from:
FaST-LMM runs on Python 3.8, 3.9, & 3.10. It runs on x64 on Linux, Windows, and Mac.
A older C++ version, including Windows binary, Linux binary, and source, supports univariate GWAS and limited epistatic testing.
PySnpTools is a Python library for reading and manipulating genetic data. It efficiently reads genetic PLINK formats (including *.bed/bim/fam files) and the BGEN format. It also efficiently reads parts of files, reads kernel data, standardizes data, manipulates data in-memory, and scales to cluster-sized data.
PySnpTools runs on Python 3.8, 3.9, 3.10 & 3.11.
It runs on x64 on Linux and Windows. On Mac, it runs on both x64 and ARM.
Learn more about PySnpTools and install from:
Data Transformations/Pre-processing for GWAS
Epigenetic Cellular Heterogeneity Correction
Epistatic Genome-Wide Association
GWAS for “Functional Traits” such as Longitudinal Traits