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: | 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 + fileLICENSE |
| URL: | https://zachariahmclean.github.io/trace/ |
| NeedsCompilation: | no |
| Citation: | trace citation info |
| Materials: | README,NEWS |
| CRAN checks: | trace results |
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