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LD

Summary Table

NAME CITATION YEAR
LDlinkR Myers TA, Chanock SJ, Machiela MJ. (2020) LDlinkR: An R package for rapidly calculating linkage disequilibrium statistics in diverse populations Front. Genet., 11 () 157. doi:10.3389/fgene.2020.00157. PMID 32180801 2020
Ldlink Machiela MJ, Chanock SJ. (2015) LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants Bioinformatics, 31 (21) 3555-3557. doi:10.1093/bioinformatics/btv402. PMID 26139635 2015
haploview Barrett JC, Fry B, Maller J, Daly MJ. (2005) Haploview: analysis and visualization of LD and haplotype maps Bioinformatics, 21 (2) 263-265. doi:10.1093/bioinformatics/bth457. PMID 15297300 2005

LDlinkR

  • NAME : LDlinkR
  • SHORT NAME : LDlinkR
  • FULL NAME : LDlinkR
  • DESCRIPTION : An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations
  • URL : https://cran.r-project.org/web/packages/LDlinkR/index.html
  • TITLE : LDlinkR: An R package for rapidly calculating linkage disequilibrium statistics in diverse populations
  • DOI : 10.3389/fgene.2020.00157
  • ABSTRACT : Genomic research involving human genetics and evolutionary biology relies heavily on linkage disequilibrium (LD) to investigate population-specific genetic structure, functionally map regions of disease susceptibility and uncover evolutionary history. Interactive and powerful tools are needed to calculate population-specific LD estimates for integrative genomics research. LDlink is an interactive suite of web-based tools developed to query germline variants in 1000 Genomes Project population groups of interest and generate interactive tables and plots of LD estimates. As an expansion to this resource, we have developed an R package, LDlinkR, designed to rapidly calculate statistics for large lists of variants and LD attributes that eliminates the time needed to perform repetitive requests from the web-based LDlink tool. LDlinkR accelerates genomic research by providing efficient and user-friendly functions to programmatically interrogate and download pairwise LD estimates from expansive lists of genetic variants. LDlinkR is a free and publicly available R package that can be installed from the Comprehensive R Archive Network (CRAN) or downloaded from https://github.com/CBIIT/LDlinkR.
  • CITATION : Myers TA, Chanock SJ, Machiela MJ. (2020) LDlinkR: An R package for rapidly calculating linkage disequilibrium statistics in diverse populations Front. Genet., 11 () 157. doi:10.3389/fgene.2020.00157. PMID 32180801
  • JOURNAL_INFO : Frontiers in genetics ; Front. Genet. ; 2020 ; 11 ; ; 157
  • PUBMED_LINK : 32180801
  • NAME : Ldlink
  • SHORT NAME : Ldlink
  • FULL NAME : Ldlink
  • DESCRIPTION : 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.
  • URL : https://ldlink.nci.nih.gov/?tab=home
  • TITLE : LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants
  • DOI : 10.1093/bioinformatics/btv402
  • ABSTRACT : UNLABELLED: Assessing linkage disequilibrium (LD) across ancestral populations is a powerful approach for investigating population-specific genetic structure as well as functionally mapping regions of disease susceptibility. Here, we present LDlink, a web-based collection of bioinformatic modules that query single nucleotide polymorphisms (SNPs) in population groups of interest to generate haplotype tables and interactive plots. Modules are designed with an emphasis on ease of use, query flexibility, and interactive visualization of results. Phase 3 haplotype data from the 1000 Genomes Project are referenced for calculating pairwise metrics of LD, searching for proxies in high LD, and enumerating all observed haplotypes. LDlink is tailored for investigators interested in mapping common and uncommon disease susceptibility loci by focusing on output linking correlated alleles and highlighting putative functional variants. AVAILABILITY AND IMPLEMENTATION: LDlink is a free and publically available web tool which can be accessed at http://analysistools.nci.nih.gov/LDlink/. CONTACT: mitchell.machiela@nih.gov.
  • CITATION : Machiela MJ, Chanock SJ. (2015) LDlink: a web-based application for exploring population-specific haplotype structure and linking correlated alleles of possible functional variants Bioinformatics, 31 (21) 3555-3557. doi:10.1093/bioinformatics/btv402. PMID 26139635
  • JOURNAL_INFO : Bioinformatics (Oxford, England) ; Bioinformatics ; 2015 ; 31 ; 21 ; 3555-3557
  • PUBMED_LINK : 26139635

haploview

  • NAME : haploview
  • SHORT NAME : haploview
  • FULL NAME : haploview
  • DESCRIPTION : Haploview is designed to simplify and expedite the process of haplotype analysis by providing a common interface to several tasks relating to such analyses.
  • URL : https://www.broadinstitute.org/haploview/haploview
  • TITLE : Haploview: analysis and visualization of LD and haplotype maps
  • DOI : 10.1093/bioinformatics/bth457
  • ABSTRACT : UNLABELLED: Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface. AVAILABILITY: http://www.broad.mit.edu/mpg/haploview/ CONTACT: jcbarret@broad.mit.edu
  • CITATION : Barrett JC, Fry B, Maller J, Daly MJ. (2005) Haploview: analysis and visualization of LD and haplotype maps Bioinformatics, 21 (2) 263-265. doi:10.1093/bioinformatics/bth457. PMID 15297300
  • JOURNAL_INFO : Bioinformatics (Oxford, England) ; Bioinformatics ; 2005 ; 21 ; 2 ; 263-265
  • PUBMED_LINK : 15297300