ArticleBioinformatics (Oxford, England)2021
svpluscnv: analysis and visualization of complex structural variation data.
Article in Bioinformatics (Oxford, England), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A Systematic Review of the Advances and New Insights into Copy Number Variations in Plant Genomes.Plants (Basel, Switzerland) · 2025Review
- A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.Cancer cell · 2024Article
- BARD1 germline variants induce haploinsufficiency and DNA repair defects in neuroblastoma.Journal of the National Cancer Institute · 2024Article
- Subclonal Somatic Copy-Number Alterations Emerge and Dominate in Recurrent Osteosarcoma.Cancer research · 2023Article
- Integrative Genomic Analyses Identify LncRNA Regulatory Networks across Pediatric Leukemias and Solid Tumors.Cancer research · 2023Article
- Article
- Subclonal somatic copy number alterations emerge and dominate in recurrent osteosarcoma.bioRxiv : the preprint server for biology · 2023Article
- Metabolism-associated molecular classification ofFrontiers in genetics · 2023Article
- The R Language: An Engine for Bioinformatics and Data Science.Life (Basel, Switzerland) · 2022Review
- DriverFuse: An R package for analysis of next-generation sequencing datasets to identify cancer driver fusion genes.PloS one · 2022Article
- Current status of structural variation studies in plants.Plant biotechnology journal · 2021Review
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
motivationDespite widespread prevalence of somatic structural variations (SVs) across most tumor types, understanding of their molecular implications often remains poor. SVs are extremely heterogeneous in size and complexity, hindering the interpretation of their pathogenic role. Tools integrating large SV datasets across platforms are required to fully characterize the cancer's somatic landscape.
resultssvpluscnv R package is a swiss army knife for the integration and interpretation of orthogonal datasets including copy number variant segmentation profiles and sequencing-based structural variant calls. The package implements analysis and visualization tools to evaluate chromosomal instability and ploidy, identify genes harboring recurrent SVs and detects complex rearrangements such as chromothripsis and chromoplexia. Further, it allows systematic identification of hot-spot shattered genomic regions, showing reproducibility across alternative detection methods and datasets. AVAILABILITY AND IMPLEMENTATION: https://github.com/ccbiolab/svpluscnv. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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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.