ArticleBioinformatics (Oxford, England)2020
CNVRanger: association analysis of CNVs with gene expression and quantitative phenotypes.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers, 1 of them a synthesis that pooled it.
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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.
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Who cites it
21 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Pituitary neuroendocrine tumors with PIT1/SF1 co-expression show distinct clinicopathological and molecular features.Acta neuropathologica · 2024Pooled it
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Integration of GWAS and eQTL analysis reveals regulatory CNVs for fatty acid traits in cattle.iScience · 2026Article
- Frizzled-1 amplification promotes fibrosis in the gastric tumor microenvironment through the activation of fibroblasts via the SLIT2/ROBO1 axis.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- Genome-Wide Analyses of Copy Number Variants in 751 Populus trichocarpa Individuals From Natural Populations.Genome biology and evolution · 2025Article
- Detecting and characterizing copy number variation in a large commercial U.S. Holstein cattle population.BMC genomics · 2025Article
- Efficient and easy gene expression and genetic variation data analysis and visualization using exvar.Scientific reports · 2025Article
- Multi-tool copy number detection highlights common body size-associated variants in miniature pig breeds from different geographical regions.BMC genomics · 2025Article
- High level of aneuploidy and recurrent loss of chromosome 11 as relevant features of somatotroph pituitary tumors.Journal of translational medicine · 2024Article
- Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China's Native Pig Breeds via Whole-Genome Resequencing.International journal of molecular sciences · 2024Article
- Genomic landscape and distinct molecular subtypes of primary testicular lymphoma.Journal of translational medicine · 2024Article
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- Genetic Association Analysis of Copy Number Variations for Meat Quality in Beef Cattle.Foods (Basel, Switzerland) · 2023Article
- Copy Number Variation onMicrobiology spectrum · 2023Article
- Curated single cell multimodal landmark datasets for R/Bioconductor.PLoS computational biology · 2023Article
- RaggedExperiment: the missing link between genomic ranges and matrices in Bioconductor.Bioinformatics (Oxford, England) · 2023Article
- Evaluation and Comparison of Multi-Omics Data Integration Methods for Subtyping of Cutaneous Melanoma.Biomedicines · 2022Article
- MethylMasteR: A Comparison and Customization of Methylation-Based Copy Number Variation Calling Software in Cancers Harboring Large Scale Chromosomal Deletions.Frontiers in bioinformatics · 2022Article
- Genome-wide detection of CNVs and their association with performance traits in broilers.BMC genomics · 2021Article
Corrections and comments
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
summaryCopy number variation (CNV) is a major type of structural genomic variation that is increasingly studied across different species for association with diseases and production traits. Established protocols for experimental detection and computational inference of CNVs from SNP array and next-generation sequencing data are available. We present the CNVRanger R/Bioconductor package which implements a comprehensive toolbox for structured downstream analysis of CNVs. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and genome-wide association analysis with gene expression and quantitative phenotypes. AVAILABILITY AND IMPLEMENTATION: http://bioconductor.org/packages/CNVRanger.
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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.