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trace: Tandem Repeat Analysis by Capillary Electrophoresis (original) (raw)

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 ORCID iD [aut, cre, cph], Kevin Correia [aut], Andrew Jiang [ctb]
Maintainer: Zachariah McLean <zachariah.louis.mclean at gmail.com>
License: MIT + file
URL: https://zachariahmclean.github.io/trace/
NeedsCompilation: no
Citation: trace citation info
Materials: README, NEWS
CRAN checks: trace results

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