regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests

By Bernat Gel, A. Díez-Villanueva, Eduard Serra, M. Buschbeck, M. Peinado, R. Malinverni. Bioinform., 2015

509 citations recorded by the source corpus.

Motivation: Statistically 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

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/70dab3ba9f04130a43bdb34b95e62c473719e87d

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In Genetics

1. Benjamin M. Neale
2. Mark J. Daly
3. L. Weiss
4. Li Zhan
5. J. Kosmicki
6. C. Betancur
7. Silvia De Rubeis
8. Kaitlin E. Samocha

In Molecular Biology

1. Li Zhan
2. Meijun Chen
3. Tianzhi Wu
4. Erqiang Hu
5. Shuangbing Xu
6. Lin Li
7. L. Weiss
8. Zijing Xie

Citations in the corpus

• karyoploteR: an R/Bioconductor package to plot customizable genomes displaying arbitrary data (2017, methodology): “Except for the additional chr parameter, they mimic the behaviour of their base graphics counterparts including the usage of most of the standard graphical parameters.”
• Exploring Epigenomic Datasets by ChIPseeker (2022, methodology): “…annotation with a single dataset; ngs.plot (Shen, Shao, Liu, & Nestler, 2014) and deeptools2 (Ramírez et al., 2016), which only present the visualization of metaplots and heatmaps; and regioneR (Gel et al., 2016), which supplies the comparison of genomic regions in the absence of a database.”
• Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2019, methodology): “A permutation-based approach with 1,000 random permutations was used to determine statistical significance of the overlap between genomic coordinates for GER and NC genes with CHD8-binding sites using the R package regioneR (Gel et al., 2016).”