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regioneR specifications

Information


Unique identifier OMICS_10179
Name regioneR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Different BED-like R objects and file formats can be used as input to any function in regioneR.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.12.0
Stability Stable
Requirements
methods, stats, parallel, graphics, IRanges, GenomicRanges, utils, testthat, S4Vectors, GenomeInfoDb, rtracklayer, BiocStyle, BSgenome, knitr, BSgenome.Hsapiens.UCSC.hg19.masked, memoise
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Bernat Gel

Publication for regioneR

regioneR citations

 (8)
library_books

Endothelial cell differentiation is encompassed by changes in long range interactions between inactive chromatin regions

2017
Nucleic Acids Res
PMCID: 5829566
PMID: 29216379
DOI: 10.1093/nar/gkx1214

[…] residing in active compartments in HUVECs. Fold changes from 20 different random sets were pooled together for visualization. To analyze the enrichment of TFs binding to specific active compartments, regioneR software was used as described above, except that regions were divided to specific active compartments, all active compartments, all inactive compartments and specific inactive compartments. […]

library_books

Hit and run epigenetic editing prevents senescence entry in primary breast cells from healthy donors

2017
Nat Commun
PMCID: 5684409
PMID: 29133799
DOI: 10.1038/s41467-017-01078-2

[…] and calculate significant DMRs. All downstream analysis was conducted using the hg19/GRCh37 human genome assembly. Annotation of DMRs and significant overlap at genomic features was calculated using regioneR (v. 1.8.0). PCA analysis was performed using DNA methylation data from all probes. […]

library_books

Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome wide repressive impact on transcription

2017
BMC Plant Biol
PMCID: 5639751
PMID: 29025411
DOI: 10.1186/s12870-017-1108-1

[…] 100 repetitions to get a statistical representation of the distribution of the “random” genes.The association between differentially expressed genes and TE was evaluated by permutation test using the regioneR R package v1.2.0 []. Up- and down-regulated genes were separated and for each group the distance from TE was compared to the average distance of the other genes in the genome by permutation t […]

library_books

Linker histone H1 prevents R loop accumulation and genome instability in heterochromatin

2017
Nat Commun
PMCID: 5561251
PMID: 28819201
DOI: 10.1038/s41467-017-00338-5

[…] Peak location and coverage plots were generated with the htSeqTools package version 1.20.0. Permutation tests to assess enrichment of repeated elements among identified peaks were performed with the regioneR package version 1.2.3, using the UCSC dm3 RepeatMasker track (March 2017).For ChIP-qPCR, triplicates from two independent biological replicates were subjected to SYBR Green I-based real-time […]

library_books

A comprehensive custom panel design for routine hereditary cancer testing: preserving control, improving diagnostics and revealing a complex variation landscape

2017
Sci Rep
PMCID: 5209725
PMID: 28051113
DOI: 10.1038/srep39348

[…] utationTaster, PROVEAN, CADD). All information, including coverage metrics, variants, variant quality estimators and annotations, was stored in a PostgreSQL database. Variants were filtered using the regioneR bioconductor package according to the clinical indication prior to generating the variant lists. The preliminary algorithm for exon-level copy-number estimation includes different normalizati […]

library_books

Systematic Profiling of Short Tandem Repeats in the Cattle Genome

2016
Genome Biol Evol
PMCID: 5381564
PMID: 28172841
DOI: 10.1093/gbe/evw256

[…] <10 were dropped here) (). To assess significance for the analyses of regions, we performed 10,000 times permutation tests to get empirical P-values for these overlaps using an R/Bioconductor package regioneR (). To further explore the selection characteristics of STRs, we employed the recently developed ksk method; ksk(20)2 values were estimated with window size 100,000 and step size 5000 as desc […]

Citations

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regioneR institution(s)
Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Campus Can Ruti, Badalona, Spain; Josep Carreras Institute for Leukaemia Research (IJC), Campus ICO-HGTP, Campus Can Ruti, Badalona, Spain
regioneR funding source(s)
This work has been supported by the Spanish Ministry of Economy and Competitiveness (SAF2012/39749; SAF2011/23638; RYC2010/07337; PTC2011/1091) and the Carlos III Health Institute (ISCIII-RTICC RD12/0036/008; PI11/1609; PI14/00577) all within the “Plan Nacional de I+D+I 2008-2011” and “Plan Estatal de I+D+I 2013-2016” and co-financed with FEDER funds; the Goverment of Catalonia (2009 SGR 290; 2014 SGR 338) and the Asociación Española Contra el Cáncer (AECC).

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