e-journal

POPGENREPORT: simplifying basic population genetic analyses in R

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1. Using scripting languages such as R to perform population genetic analyses can improve the reproducibility
of research, but usingRcan be challenging for many researchers due to its steep learning curve.
2. POPGENREPORT is a new R package that simplifies performing population genetics analyses in R, through the
use of a new report-generating function. The function POPGENREPORT allows users to perform up to 13 pre-defined
and 1 user-defined analyses through the use of a single command line. Each analysis generates figures and tables
that are incorporated into a PDF report and are also made available as individual files (figures are provided inmultiple formats, table contents are provided as CSV files).
3. The package includes new R functions that simplify the importation of data from a spreadsheet file, examine
allele distributions across populations and loci and identify private alleles, determine pairwise individual genetic
distances using themethods of Smouse and Peakall (1999) andKosman and Leonard (2005), respectively, detect
the presence of null alleles, calculate allelic richness, and test for spatial autocorrelation in genotypes using the methods of Smouse and Peakall (1999).
4. The package has a modular structure that makes the process of adding new functionality straightforward. To
facilitate the addition of user-designed functions, the package includes a fully customizable module that can be
automatically included in the PDF report.
5. To support users not experienced in R, the website (www.popgenreport.org) has a tutorial for the package
and a downloadable, portable version of the package with LaTeX pre-configured for the Windows operating
system.

Key-words: ecological genetics, population genetics, software, bioinformatics, quantitative genetics,
individual pairwise genetic distances

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Ketersediaan

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Informasi Detail

Judul Seri

Methods in Ecology and Evolution

No. Panggil

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Penerbit

: British Ecological Society., 2014

Deskripsi Fisik

Methods in Ecology and Evolution 2014, 5, 384–387

Bahasa

English

ISBN/ISSN

doi: 10.1111/2041-21

Klasifikasi

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Tipe Isi

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Tipe Media

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Tipe Pembawa

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Edisi

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Subjek

BIOLOGI

Info Detail Spesifik

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Pernyataan Tanggungjawab

Wati/Agus

Versi lain/terkait

Lampiran Berkas

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