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argyle specifications

Information


Unique identifier OMICS_17746
Name argyle
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 0.2.0
Stability Stable
Maintained Yes

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Publication for argyle

argyle citations

 (5)
library_books

The genomic ancestry, landscape genetics and invasion history of introduced mice in New Zealand

2018
R Soc Open Sci
PMCID: 5792881
PMID: 29410804
DOI: 10.1098/rsos.170879

[…] The software used in the research can be located as follows:Plink 1.9: https://www.cog-genomics.org/plink2;argyle: https://github.com/andrewparkermorgan/argyle;Admixture: https://www.genetics.ucla.edu/software/admixture/download.html;Tess3r: https://github.com/cayek/TESS3/tree/master/tess3r;Ape: https://cr […]

library_books

Genomes of the Mouse Collaborative Cross

2017
Genetics
PMCID: 5499171
PMID: 28592495
DOI: 10.1534/genetics.116.198838

[…] rations of the Mouse Universal Genotyping Array, MUGA, MegaMUGA, and GigaMUGA (GeneSeek, Lincoln, NE) (; ). Genotypes were called using Illumina BeadStudio (Illumina, Carlsbad, CA) and processed with Argyle (). All genotypes are available at Zenodo (https://doi.org/10.5281/zenodo.377036). […]

library_books

Allelic Variation in the Toll Like Receptor Adaptor Protein Ticam2 Contributes to SARS Coronavirus Pathogenesis in Mice

2017
PMCID: 5473747
PMID: 28592648
DOI: 10.1534/g3.117.041434

[…] array hybridization on the MUGA array (). Genotypes were called by the vendor using the GenCall algorithm implemented in the Illumina BeadStudio software. Quality checks and further analysis used the argyle package () for the R environment (www.cran.r-project.org). […]

library_books

Diversity Outbred Mice at 21: Maintaining Allelic Variation in the Face of Selection

2016
PMCID: 5144960
PMID: 27694113
DOI: 10.1534/g3.116.035527

[…] sing the same samples for training but retaining all 46 probes (MegaMUGA) or 32 probes (GigaMUGA) mapping to the mitochondrial genome. Haplogroup assignment routines are implemented in the R package “argyle” (). […]

library_books

The Mouse Universal Genotyping Array: From Substrains to Subspecies

2015
PMCID: 4751547
PMID: 26684931
DOI: 10.1534/g3.115.022087

[…] (both raw and processed) for 522 reference samples are available for download from http://csbio.unc.edu/MUGA. Routines for quality checks and intensity normalization are implemented in the R package argyle, described elsewhere (, this issue), and available for download from GitHub (https://github.com/andrewparkermorgan/argyle).The GigaMUGA genotyping service is provided exclusively by Neogen Inc. […]

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argyle institution(s)
Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
argyle funding source(s)
This work was supported in part by NIH grants F30MH103925 (APM), U19AI100625 (FPMV), U42OD010924 (Terry Magnuson), and the UNC Bioinformatics and Computational Biology Training Grant (T32GM067553).

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