PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
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Updated
Jun 27, 2022 - C++
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
Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
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.
LDlinkR
🔖 Get SNP proxies from the 1000 Genomes Project.
Fast calculations of linkage-disequilibrium in large-scale human cohorts
Adjacency-constrained hierarchical clustering of a similarity matrix
Modeling and Analysis of (Statistical) Genetics data in python
📙 Explore 1000 Genomes variant data with JavaScript.
ldshrink: a one-stop R package for shrinkage estimation of linkage disequilibrium
LDlinkR: An R package for calculating linkage disequilibrium in human populations of interest
Efficient Local Ancestry Inference
This method incorporates dense linkage disequilibrium block structure of SNPs for prioritizing a set of genetic variants using GWAS summary statisticis before performing fine-mapping.
A python library to develop genomic data simulators
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.
ld-tools: toolkit for linkage disequilibrium calculation designed to work locally
By leveraging ensemble learning, this program can be used to analyze the Linkage Disequilibrium between SNPs in each Indonesian rice chromosomes. Developed using Python 3.9.12.
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