ArticleBioinformatics (Oxford, England)2019
gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks.
Article in Bioinformatics (Oxford, England), 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Constitution and function of intergenic genome regions in cultivated versus annual wild soybean in China.Journal of integrative plant biology · 2026Article
- Probabilities of two alleles being identity by state at unobserved loci predicted by observed loci in cattle populations.Scientific reports · 2026Article
- The PeachSNP170K array facilitates insights into a large-scale population relatedness and genetic impacts on citrate content and flowering time.Communications biology · 2025Article
- Determinant-based grouping of SNPs and its application for detecting disease-associated genomic loci.NAR genomics and bioinformatics · 2025Article
- Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat.The plant genome · 2025Article
- RegionScan: a comprehensive R package for region-level genome-wide association testing with integration and visualization of multiple-variant and single-variant hypothesis testing.Bioinformatics advances · 2025Article
- Elucidation of the genetic architecture of water absorption capacity in hard winter wheat through genome wide association study.The plant genome · 2024Article
- Exploration of quality variation and stability of hybrid rice under multi-environments.Molecular breeding : new strategies in plant improvement · 2024Article
- Genetic analysis of pericarp pigmentation variation in Corn Belt dent maize.G3 (Bethesda, Md.) · 2023Article
- Identification of genetic variants associated with anterior cruciate ligament rupture and AKC standard coat color in the Labrador Retriever.BMC genomic data · 2023Article
- GWLD: an R package for genome-wide linkage disequilibrium analysis.G3 (Bethesda, Md.) · 2023Article
- Expanding the application of haplotype-based genomic predictions to the wild: A case of antibody response against Teladorsagia circumcincta in Soay sheep.BMC genomics · 2023Article
- The effect of cycles of genomic selection on the wheat (T. aestivum) genome.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- SNP- and haplotype-based single-step genomic predictions for body weight, wool, and reproductive traits in North American Rambouillet sheep.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2023Article
- Multi-locus genome-wide association studies reveal the genetic architecture ofFrontiers in plant science · 2023Article
- Haplotype blocks for genomic prediction: a comparative evaluation in multiple crop datasets.Frontiers in plant science · 2023Article
- Identification of loci associated with water use efficiency and symbiotic nitrogen fixation in soybean.Frontiers in plant science · 2023Article
- Are Copy Number Variations within theAnimals : an open access journal from MDPI · 2022Article
- Root angle in maize influences nitrogen capture and is regulated by calcineurin B-like protein (CBL)-interacting serine/threonine-protein kinase 15 (ZmCIPK15).Plant, cell & environment · 2022Article
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6 authors.
Funding
Abstract
summaryFor the analysis of high-throughput genomic data produced by next-generation sequencing (NGS) technologies, researchers need to identify linkage disequilibrium (LD) structure in the genome. In this work, we developed an R package gpart which provides clustering algorithms to define LD blocks or analysis units consisting of SNPs. The visualization tool in gpart can display the LD structure and gene positions for up to 20 000 SNPs in one image. The gpart functions facilitate construction of LD blocks and SNP partitions for vast amounts of genome sequencing data within reasonable time and memory limits in personal computing environments. AVAILABILITY AND IMPLEMENTATION: The R package is available at https://bioconductor.org/packages/gpart. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.