regioneR protocols

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 1.0.3
Stability Stable
Requirements memoise, GenomicRanges, BSgenome, rtracklayer, parallel
Maintained Yes

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Documentation


Maintainer


  • person_outline Bernat Gel <>

Publication for regioneR

regioneR IN pipelines

 (2)
2018
PMCID: 5785814
PMID: 29370772
DOI: 10.1186/s12864-018-4444-0

[…] enrichment analysis was performed considering q-values calculated from a fdr test, and pathways with q-values < 0.1 were considered significant., qtl overlap analysis was carried out using the regioner package [73]. from 190 traits, a subset of 62 representing the most relevant in poultry were selected for this analysis. a permutation test was performed to evaluate the significant […]

2017
PMCID: 5576322
PMID: 28851275
DOI: 10.1186/s12864-017-4083-x

[…] and (a) genes encoding candidate secreted effector proteins, and (b) all genes contained within secondary metabolism gene clusters were analysed using permutation tests implemented in the r package regioner [54]. the mean distance between each gene in each functional category and the nearest te was compared to the mean distance of a random sample of genes taken from the whole genome. ten […]

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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