ReviewBioinformatics (Oxford, England)2023
crosshap: R package for local haplotype visualization for trait association analysis.
Review in Bioinformatics (Oxford, England), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
9 citing papers in PubMed.
- Dissection of local haplotype diversity at soybean rust loci reveals resistance-associated and context-dependent variation patterns in diverse germplasm.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Trait Association for Flowering Time in Lentil from Global Multi-Environment Data Using GWAS and Machine Learning.Plants (Basel, Switzerland) · 2026Article
- Intraspecific genome size variation is attributed to adaptive silencing of transposable elements in Hordeum species.Molecular biology and evolution · 2026Article
- Genome-wide exploration of bacterial leaf blight resistance and fine mapping of major resistance gene (Bb13) in upland cotton (Gossypium hirsutum L.).The plant genome · 2026Article
- Haplotype applications in genomic selection.Genome biology · 2026Review
- HaploVar: An R package for defining local haplotype variants for trait association and trait prediction analyses.Bioinformatics (Oxford, England) · 2025Article
- Integrating multi-omics and machine learning for disease resistance prediction in legumes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Review
- Synergistic potential of CDH3 in targeting CRC metastasis and enhancing immunotherapy.BMC cancer · 2025Article
- Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean.The plant genome · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryGenome-wide association studies (GWAS) excels at harnessing dense genomic variant datasets to identify candidate regions responsible for producing a given phenotype. However, GWAS and traditional fine-mapping methods do not provide insight into the complex local landscape of linkage that contains and has been shaped by the causal variant(s). Here, we present crosshap, an R package that performs robust density-based clustering of variants based on their linkage profiles to capture haplotype structures in a local genomic region of interest. Following this, crosshap is equipped with visualization tools for choosing optimal clustering parameters (ɛ) before producing an intuitive figure that provides an overview of the complex relationships between linked variants, haplotype combinations, phenotype, and metadata traits. AVAILABILITY AND IMPLEMENTATION: The crosshap package is freely available under the MIT license and can be downloaded directly from CRAN with R >4.0.0. The development version is available on GitHub alongside issue support (https://github.com/jacobimarsh/crosshap). Tutorial vignettes and documentation are available (https://jacobimarsh.github.io/crosshap/).
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Registered trials
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.