PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files

Causal Mixture Model for GWAS summary statistics

LDlinkR

Fast calculations of linkage-disequilibrium in large-scale human cohorts

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

R front-end for TASSEL 5

🔖 Get SNP proxies from the 1000 Genomes Project.

LDlink is a suite of web-based applications designed to easily and efficiently interrogate linkage disequilibrium in population groups. Each included application is specialized for querying and displaying unique aspects of linkage disequilibrium.

Efficient Local Ancestry Inference

Modeling and Analysis of (Statistical) Genetics data in python

Adjacency-constrained hierarchical clustering of a similarity matrix

Genomewide Epistasis Analysis on Bacteria

ldshrink: a one-stop R package for shrinkage estimation of linkage disequilibrium

📙 Explore 1000 Genomes variant data with JavaScript.

This is web server API for http://topld.genetics.unc.edu

ld-tools: toolkit for linkage disequilibrium calculation designed to work locally

A python library to develop genomic data simulators

GWAS Pre-Processing Pipeline

Get information about direction of agreement for any two lists of SNPs, based on LDlink and plink

Generating a weighed average of LDSTORE matrices for locus-based fine-mapping.