linkage-disequilibrium
There are 34 repositories under linkage-disequilibrium topic.
BGI-shenzhen/PopLDdecay
PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format(VCF) files
precimed/mixer
Causal Mixture Model for GWAS summary statistics
CBIIT/LDlinkR
LDlinkR
mklarqvist/tomahawk
Fast calculations of linkage-disequilibrium in large-scale human cohorts
RajLabMSSM/echolocatoR
Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.
maize-genetics/rTASSEL
R front-end for TASSEL
slowkow/proxysnps
:bookmark: Get SNP proxies from the 1000 Genomes Project.
CBIIT/nci-webtools-dceg-linkage
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.
pneuvial/adjclust
Adjacency-constrained hierarchical clustering of a similarity matrix
shz9/magenpy
Modeling and Analysis of (Statistical) Genetics data in python
Sudaraka88/LDWeaver
Genomewide Epistasis Analysis on Bacteria
stephenslab/ldshrink
ldshrink: a one-stop R package for shrinkage estimation of linkage disequilibrium
haplotype/ELAI
Efficient Local Ancestry Inference
slowkow/snpbook
:orange_book: Explore 1000 Genomes variant data with JavaScript.
linnabrown/topld_api
This is web server API for http://topld.genetics.unc.edu
tbrunetti/GP3
GWAS Pre-Processing Pipeline
PlatonB/ld-tools
ld-tools: toolkit for linkage disequilibrium calculation designed to work locally
remytuyeras/HaploDynamics
A python library to develop genomic data simulators
MikeDacre/LDDirection
Get information about direction of agreement for any two lists of SNPs, based on LDlink and plink
Pintaius/LDmergeFM
Generating a weighed average of LDSTORE matrices for locus-based fine-mapping.
machiela-lab/LDlinkR
Calculating linkage disequilibrium in human populations of interest
RajLabMSSM/echoLD
echoverse module: LD downloading and processing
scikal/LD-CHASE
A tool for linkage disequilibrium-informed comparison of haplotypes among sibling embryos.
TomMakesThings/Wright-Fisher-Simulator
Simulator for the Wright-Fisher model of genetic drift for haploid and diploid populations
cmomo/LocNet
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.
joe-nas/haploplotR
Visualizing Linkage Disequilibrium using 1000 Genomes Data
NicholasDominic/Stochastic-VIF-ID-Rice-SNPs
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.
rendy0505/LD-heterogeneity
Impact of LD regional heterogeneity on genome prediction and heritability estimation in livestock
Soton-CompGen/LDMAP
LDMAP software for mapping linkage disequilibrium using the Malecot-Morton model.
Soton-CompGen/zalpha
R package for the zalpha suite of selection statistics
timyers/ldlinkr
LDlinkR: An R package for calculating linkage disequilibrium in human populations of interest
dhimmel/ensembl-api
Working wiht the Ensembl Perl API
hernanmd/ldHeatmap_equine.2018
Plot .ld with LDHeatmap (first case applied to Equine 65k Microarray)
vforget/r-sq-prime
Implement R-prime measure of linkage disequilibrium