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Oxford University Press (OUP), Bioinformatics, 17(35), p. 3194-3195, 2019

DOI: 10.1093/bioinformatics/btz030

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admixr—R package for reproducible analyses using ADMIXTOOLS

Journal article published in 2019 by Martin Petr ORCID, Benjamin Vernot ORCID, Janet Kelso ORCID
This paper was not found in any repository, but could be made available legally by the author.
This paper was not found in any repository, but could be made available legally by the author.

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Data provided by SHERPA/RoMEO

Abstract

Abstract Summary We present a new R package admixr, which provides a convenient interface for performing reproducible population genetic analyses (f3, D, f4, f4-ratio, qpWave and qpAdm), as implemented by command-line programs in the ADMIXTOOLS software suite. In a traditional ADMIXTOOLS workflow, the user must first generate a set of text configuration files tailored to each individual analysis, often using a combination of shell scripting and manual text editing. The non-tabular output files then need to be parsed to extract values of interest prior to further analyses. Our package simplifies this process by automating all low-level configuration and parsing steps, making analyses as simple as running a single R command. Furthermore, we provide a set of R functions for processing, filtering and manipulating datasets in the EIGENSTRAT format. By unifying all steps of the workflow under a single R framework, this package enables the automation of analytic pipelines, significantly improving the reproducibility of population genetic studies. Availability and implementation The source code of the R package is available under the MIT license. Installation instructions, reference manual and a tutorial can be found on the package website at https://bioinf.eva.mpg.de/admixr. Supplementary information Supplementary data are available at Bioinformatics online.