Package: trace
Title: Tandem Repeat Analysis by Capillary Electrophoresis
Version: 1.0.0
Authors@R: c(
    person("Zachariah", "McLean", , "zachariah.louis.mclean@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-0968-0538")),
    person("Kevin", "Correia", role = "aut"),
    person("Andrew", "Jiang", role = "ctb")
  )
Description: 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>).
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.3
Suggests: knitr, dplyr, ggplot2, shinytest2, testthat (>= 3.0.0)
Config/testthat/edition: 3
Imports: graphics, grDevices, lme4, methods, mgcv, plotly, pracma,
        seqinr, shiny, stats, utils, yaml
VignetteBuilder: knitr
Depends: R (>= 3.5)
LazyData: true
URL: https://zachariahmclean.github.io/trace/
NeedsCompilation: no
Packaged: 2025-12-22 16:26:20 UTC; gusella_lab
Author: Zachariah McLean [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-0968-0538>),
  Kevin Correia [aut],
  Andrew Jiang [ctb]
Maintainer: Zachariah McLean <zachariah.louis.mclean@gmail.com>
Repository: CRAN
Date/Publication: 2025-12-22 17:00:02 UTC
Built: R 4.4.3; ; 2026-03-02 19:05:33 UTC; windows
