trace: Tandem Repeat Analysis by Capillary Electrophoresis

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: 1.0.0
Depends: R (≥ 3.5)
Imports: graphics, grDevices, lme4, methods, mgcv, plotly, pracma, seqinr, shiny, stats, utils, yaml
Suggests: knitr, dplyr, ggplot2, shinytest2, testthat (≥ 3.0.0)
Published: 2025-12-22
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 LICENSE
URL: https://zachariahmclean.github.io/trace/
NeedsCompilation: no
Citation: trace citation info
Materials: README, NEWS
CRAN checks: trace results

Documentation:

Reference manual: trace.html , trace.pdf
Vignettes: plotting_traces (source, R code)

Downloads:

Package source: trace_1.0.0.tar.gz
Windows binaries: r-devel: trace_0.6.0.zip, r-release: trace_1.0.0.zip, r-oldrel: trace_0.6.0.zip
macOS binaries: r-release (arm64): trace_1.0.0.tgz, r-oldrel (arm64): trace_1.0.0.tgz, r-release (x86_64): trace_1.0.0.tgz, r-oldrel (x86_64): trace_1.0.0.tgz
Old sources: trace archive

Linking:

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