ArticleBMC bioinformatics2023
geneHapR: an R package for gene haplotypic statistics and visualization.
Article in BMC bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 94 papers.
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94 citing papers in PubMed.
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- First survey on the occurrence, subtype distribution and circulation of the enteric protozoan Blastocystis sp. in French broiler chicken farms.Poultry science · 2026Article
- Marker-trait associations and superior haplotypes for rice straw cell wall components and their relationship with digestibility and agronomic traits.BMC plant biology · 2026Article
- Genome-wide association mapping and haplotype analysis reveal the genetic architecture of sodicity tolerance in bread wheat (Triticum aestivum L.).Scientific reports · 2026Article
- Comprehensive analysis of maBIOTECH · 2026Article
- Genetic dissection of root traits in barley identifies major QTLs and domestication signature.Plant cell reports · 2026Article
- Genome-wide association and population-tailored polygenic risk for Parkinson's disease in Taiwan.NPJ Parkinson's disease · 2026Article
- Water stress tolerance, genomic selection and identification of genomic regions in a MAGIC population of eggplant.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Genomic diversity at thePlant diversity · 2026Article
- Genome-Wide Identification and Expression Analysis of Starch Biosynthesis-Related Gene Families in Wheat.International journal of molecular sciences · 2026Article
- Genome-Wide Association Study of Yield-Related Traits and Photoperiod Response in Rice.Plants (Basel, Switzerland) · 2026Article
- Genomic dissection of iron toxicity tolerance in rice identifies key loci, candidate genes, and associated haplotypes.Scientific reports · 2026Article
34 more citing papers are in PubMed but not listed here.
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3 authors.
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Abstract
backgroundTogether with application of next-generation sequencing technologies and increased accumulation of genomic variation data in different organism species, an opportunity for effectively identification of superior alleles of functional genes to facilitate marker-assisted selection is emerging, and the clarification of haplotypes of functional genes is becoming an essential target in recent study works.
resultsIn this paper, we describe an R package 'geneHapR' developed for haplotypes identification, statistics and visualization analysis of candidate genes. This package could integrate genotype data, genomic annotating information and phenotypic variation data to clarify genotype variations, evolutionary-ship, and morphological effects among haplotypes through variants visualization, network construction and phenotypic comparison. 'geneHapR' also provides functions for Linkage Disequilibrium block analysis and visualizing of haplotypes geo-distribution.
conclusionsThe R package 'geneHapR' provided an easy-to-use tool for haplotype identification, statistic and visualization for candidate gene and will provide useful clues for gene functional dissection and molecular-assistant pyramiding of beneficial alleles of functional locus in future breeding programs.
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