karyoploteR statistics

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karyoploteR specifications

Information


Unique identifier OMICS_17189
Name karyoploteR
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.7.8
Stability Stable
Requirements
methods, stats, graphics, IRanges, GenomicRanges, Rsamtools, testthat, S4Vectors, GenomeInfoDb, rtracklayer, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, GenomicFeatures, knitr, regioneR, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, digest, pasillaBamSubset, magrittr, R(>=3.4), memoise, bamsignals, bezier
Maintained Yes

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Maintainer


  • person_outline Bernat Gel <>

Publication for karyoploteR

karyoploteR in publication

PMCID: 5805323
PMID: 29420602
DOI: 10.1371/journal.pone.0192540

[…] in plink. the calculation was done both on the whole panel of 783 cultivars, and on each of the 8 subgroups resulting from the dapc analysis. the resulting blocks were plotted on chromosomes using karyoploter r script []., genome-wide association analysis (gwa) was carried out using the weighted-mlm model in tassel (version 5.2.28, [, ]). the genetic structure matrix (used as a fixed-effect […]


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karyoploteR institution(s)
Hereditary Cancer Group, Program for Predictive and Personalized Medicine of Cancer - Germans Trias i Pujol Research Institute (PMPPC-IGTP), Badalona, Spain
karyoploteR funding source(s)
This work has been supported by: the Spanish Ministry of Science and Innovation, Carlos III Health Institute (ISCIII) (PI11/1609; PI14/00577)(RTICC RD12/0036/008) Plan Estatal de I + D + I 2013-2016, and co-financed by the FEDER program; the Government of Catalonia (2014 SGR 338); and the Spanish Association Against Cancer (AECC).

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