geneHapR: an R package for gene haplotypic statistics and visualization

Background Together 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 emergin...

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Bibliographic Details
Published in:BMC bioinformatics Vol. 24; no. 1; pp. 199 - 13
Main Authors: Zhang, Renliang, Jia, Guanqing, Diao, Xianmin
Format: Journal Article
Language:English
Published: London BioMed Central 15.05.2023
BioMed Central Ltd
Springer Nature B.V
BMC
Subjects:
Algorithms
Alleles
Analysis
Annotations
Bioinformatics
Biomedical and Life Sciences
Chromosomes
Computational Biology/Bioinformatics
Computer Appl. in Life Sciences
geneHapR
Genes
Genetic aspects
Genetic research
Genomes
Genomics
Genotype
Genotype & phenotype
Genotypes
Haplotype identification
Haplotypes
Identification
LD-block
Life Sciences
Linkage analysis
Linkage Disequilibrium
Marker assisted selection
Methods
Microarrays
Morphology
Names
Network
Next-generation sequencing
Phenotypic variations
Plant breeding
Polymorphism, Single Nucleotide
R (Programming language)
Software
Statistical analysis
Statistical software
Statistics
Visualization
Visualization (Computers)
China
Visualization
R
Haplotype identification
LD-block
geneHapR
Network
ISSN:1471-2105, 1471-2105
Online Access:Get full text
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Summary:Background Together 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. Results In 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. Conclusions The 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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ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-023-05318-9