odgi

Use when estimating SNP heritability, local heritability, or genetic architecture from GWAS summary statistics. Covers per-locus heritability partitioning, total heritability estimation, LD matrix com

2 shared topics • 2 shared operations

IMPUTE5 for genotype imputation from phased haplotypes and a reference panel. Performs fast, accurate imputation using the Li and Stephens hidden Markov model with the PBWT data structure for efficien

2 shared topics • 2 shared operations

Use when performing Mendelian randomization (MR) analyses to estimate causal effects of exposures on outcomes using genetic variants as instrumental variables. Covers two-sample MR, IVW, MR-Egger, wei

2 shared topics • 2 shared operations

rMVP GWAS analysis for plant genomics. Use when running genome-wide association studies, GWAS models (GLM, MLM, FarmCPU), SNP genotype formatting, kinship matrix calculation, population structure PCA,

2 shared topics • 2 shared operations

scikit-allel — Python package for exploratory analysis of large-scale genetic variation data. Provides data structures for genotypes, haplotypes, and allele counts (GenotypeArray, HaplotypeArray, Alle

2 shared topics • 1 shared operation