ArticleBioinformatics (Oxford, England)2022
StructuralVariantAnnotation: a R/Bioconductor foundation for a caller-agnostic structural variant software ecosystem.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- SDFA: a standardized decomposition format and toolkit for efficient analysis of structural variants in large-scale population genomic studies.Genome biology · 2025Article
- Intratumor heterogeneity of HPV integration in HPV-associated head and neck cancer.Nature communications · 2025Article
- Comparisons of performances of structural variants detection algorithms in solitary or combination strategy.PloS one · 2025Article
- Prostate cancer patient stratification by molecular signatures in the Veterans Precision Oncology Data Commons.Cold Spring Harbor molecular case studies · 2023Article
- Article
- The microtubule inhibitor eribulin demonstrates efficacy in platinum-resistant and refractory high-grade serous ovarian cancer patient-derived xenograft models.Therapeutic advances in medical oncology · 2023Article
- Whole Genome Sequencing Analysis of Effects of CRISPR/Cas9 inJournal of fungi (Basel, Switzerland) · 2022Article
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Authors and funding
3 authors.
Funding
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Abstract
summaryStructuralVariantAnnotation is an R/Bioconductor package that provides a framework for decoupling downstream analysis of structural variant breakpoints from upstream variant calling methods. It standardizes the representational format from BEDPE, or any of the three different notations supported by VCF into a breakpoint GRanges data structure suitable for use by the wider Bioconductor ecosystem. It handles both transitive breakpoints and duplication/insertion notational differences of identical variants-both common scenarios when comparing short/long read-based call sets that confound downstream analysis. StructuralVariantAnnotation provides the caller-agnostic foundation needed for a R/Bioconductor ecosystem of structural variant annotation, classification and interpretation tools able to handle both simple and complex genomic rearrangements. AVAILABILITY AND IMPLEMENTATION: StructuralVariantAnnotation is implemented in R and available for download as the Bioconductor StructuralVariantAnnotation package. Details can be found at https://www.bioconductor.org/packages/release/bioc/html/StructuralVariantAnnotation.html. It has been released under a GPL license.
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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.