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 
[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:
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