ArticleBioinformatics (Oxford, England)2023
regioneReloaded: evaluating the association of multiple genomic region sets.
Article 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 7 papers.
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Who cites it
7 citing papers in PubMed.
- 3D chromatin organisation contributes to the regulatory logic in differentiating lymphatic endothelium.EMBO reports · 2026Article
- Identification of methylation-sensitive human transcription factors using meSMiLE-seq.Nature communications · 2026Article
- Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.Cell genomics · 2026Article
- EccDNA atlas in male mice reveals features protecting genes against transcription-induced eccDNA formation.Nature communications · 2025Article
- Chromatin environment-dependent effects of DOT1L on gene expression in male germ cells.Communications biology · 2025Article
- Exploration and Enrichment Analysis of the QTLome for Important Traits in Livestock Species.Genes · 2024Article
- Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma.The Journal of clinical investigation · 2024Article
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Authors and funding
4 authors.
Funding
Abstract
motivationNext-generation sequencing methods continue improving the annotation of genomes in part by determining the distribution of features such as epigenetic marks. Evaluating and interpreting the association between genomic regions and their features has become a common and challenging analysis in genomic and epigenomic studies.
resultsWith regioneR we provided an R package allowing to assess the statistical significance of pairwise associations between genomic region sets using permutation tests. We now present the R package regioneReloaded that builds upon regioneR's statistical foundation and extends the functionality for the simultaneous analysis and visualization of the associations between multiple genomic region sets. Thus, we provide a novel discovery tool for the identification of significant associations that warrant to be tested for functional interdependence. AVAILABILITY AND IMPLEMENTATION: regioneReloaded is an R package released under an Artistic-2.0 License. The source code and documentation are freely available through Bioconductor: http://www.bioconductor.org/packages/regioneReloaded.
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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.