A pipeline for short tandem repeat instability analysis from fragment analysis data. Inputs of fsa files or peak tables, and a user supplied metadata data-frame. The package identifies ladders, calls peaks, identifies the modal peaks, calls repeats, then calculates repeat instability metrics (e.g. expansion index from Lee et al. (2010) <doi:10.1186/1752-0509-4-29>).
Version: 0.6.0 Depends: R (≥ 2.10) Imports: graphics, grDevices, lme4, methods, mgcv, plotly, pracma, seqinr, shiny, stats, utils Suggests: dplyr, ggplot2, knitr, rmarkdown, shinytest2, testthat (≥ 3.0.0) Published: 2025-03-14 DOI: 10.32614/CRAN.package.trace Author: Zachariah McLean [aut, cre, cph], Kevin Correia [aut], Andrew Jiang [ctb] Maintainer: Zachariah McLean <zachariah.louis.mclean at gmail.com> License: MIT + file LICENSE URL: https://zachariahmclean.github.io/trace/ NeedsCompilation: no Citation: trace citation info Materials: README NEWS CRAN checks: trace results Documentation: Downloads: Linking:Please use the canonical form https://CRAN.R-project.org/package=trace to link to this page.
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