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:	0.5.0
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:	2025-01-16
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:

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

Downloads:

Package source:	trace_0.5.0.tar.gz
Windows binaries:	r-devel: trace_0.5.0.zip, r-release: not available, r-oldrel: trace_0.5.0.zip
macOS binaries:	r-release (arm64): trace_0.5.0.tgz, r-oldrel (arm64): not available, r-release (x86_64): trace_0.5.0.tgz, r-oldrel (x86_64): trace_0.5.0.tgz

Linking:

Please use the canonical form https://CRAN.R-project.org/package=trace to link to this page.