ArticleBioinformatics (Oxford, England)2016
regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 379 papers.
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Who cites it
379 citing papers in PubMed.
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- A deep learning model captures position-specific effects of plant regulatory sequences and suggests genes under complex regulation.Plant physiology · 2026Article
- Genome-wide crossover analysis in the holocentric pantry moth reveals strong crossover assurance and interference during spermatogenesis.Genome research · 2026Article
- Decoding gene responsiveness to synthetic chromatin reader-actuators with multi-modal epigenomic profiling.NPJ systems biology and applications · 2026Article
- TET1 noncatalytic activity shapes the chromatin landscape associated with de novo methylation establishment in the male germline.Genes & development · 2026Article
- Genome assembly of Astatotilapia latifasciata uncovers B chromosome-linked chromatin reorganization.Heredity · 2026Article
- The hidden sources of spurious fusion transcripts in plants.Genome biology · 2026Article
- A multimodal interrogation of Broca's area in the pediatric and adult human brain.bioRxiv : the preprint server for biology · 2026Article
- Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.Cell genomics · 2026Article
- Programmed DNA elimination was present in the last common ancestor ofbioRxiv : the preprint server for biology · 2026Article
- Somatic mobility of transposons is explosive and shaped by distinct integration biases in Arabidopsis thaliana.Genome biology · 2026Article
- A Practical Framework for GT-Seq Panel Optimization.Molecular ecology resources · 2026Article
- 3D Chromatin Architecture Provides Insights Into Leaf Trait Variation Among Pear Species.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Divergent 3D genome architecture of male germ cells across vertebrates.Nature communications · 2026Article
- Integration of GWAS and eQTL analysis reveals regulatory CNVs for fatty acid traits in cattle.iScience · 2026Article
319 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationStatistically assessing the relation between a set of genomic regions and other genomic features is a common challenging task in genomic and epigenomic analyses. Randomization based approaches implicitly take into account the complexity of the genome without the need of assuming an underlying statistical model. SUMMARY: regioneR is an R package that implements a permutation test framework specifically designed to work with genomic regions. In addition to the predefined randomization and evaluation strategies, regioneR is fully customizable allowing the use of custom strategies to adapt it to specific questions. Finally, it also implements a novel function to evaluate the local specificity of the detected association. AVAILABILITY AND IMPLEMENTATION: regioneR is an R package released under Artistic-2.0 License. The source code and documents are freely available through Bioconductor (http://www.bioconductor.org/packages/regioneR). CONTACT: rmalinverni@carrerasresearch.org.
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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.