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. 2014 Jul 9;2(1):e11.
doi: 10.5334/jors.at.

Fourteen Years of R/qtl: Just Barely Sustainable

Karl W Broman  1
Affiliations

Fourteen Years of R/qtl: Just Barely Sustainable

Karl W Broman. J Open Res Softw. .

Abstract

R/qtl is an R package for mapping quantitative trait loci (genetic loci that contribute to variation in quantitative traits) in experimental crosses. Its development began in 2000. There have been 38 software releases since 2001. The latest release contains 35k lines of R code and 24k lines of C code, plus 15k lines of code for the documentation. Challenges in the development and maintenance of the software are discussed. A key to the success of R/qtl is that it remains a central tool for the chief developer's own research work, and so its maintenance is of selfish importance.

Keywords: QTL mapping; quantitative trait loci; software; sustainable software.

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Figures

Figure 1
Figure 1
Typical analysis results from R/qtl. A: LOD curves across the genome, measuring association between phenotype and genotype across, and B: Association between genotype and phenotype at the marker with the strongest association. The data are from [1]; panel B was created using the R package beeswarm.
Figure 2
Figure 2
Numbers of lines of code in released versions of R/qtl over time. (Yellow and blue correspond to R and C code, respectively; pink is for the R documentation files.)
See this image and copyright information in PMC

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