% pubman genre = article @article{item_3021896, title = {{admixr {\textendash} R package for reproducible analyses using ADMIXTOOLS}}, author = {Petr, Martin and Vernot, Benjamin and Kelso, Janet}, language = {eng}, issn = {1460-2059}, doi = {10.1093/bioinformatics/btz030}, publisher = {Oxford University Press}, address = {Oxford}, year = {2019}, date = {2019-09-01}, abstract = {{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.}}, journal = {{Bioinformatics}}, volume = {35}, number = {17}, pages = {3194--3195}, eid = {btz030}, }