Package: trace 1.0.0

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>).

Authors:Zachariah McLean [aut, cre, cph], Kevin Correia [aut], Andrew Jiang [ctb]

trace_1.0.0.tar.gz
trace_1.0.0.zip(r-4.7)trace_1.0.0.zip(r-4.6)trace_1.0.0.zip(r-4.5)
trace_1.0.0.tgz(r-4.6-any)trace_1.0.0.tgz(r-4.5-any)
trace_1.0.0.tar.gz(r-4.7-any)trace_1.0.0.tar.gz(r-4.6-any)
trace_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
trace/json (API)

# Install 'trace' in R:
install.packages('trace', repos = c('https://zachariahmclean.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zachariahmclean/trace/issues

Pkgdown/docs site:https://zachariahmclean.github.io

Datasets:

On CRAN:

Conda:

5.31 score 1 stars 204 scripts 217 downloads 20 exports 89 dependencies

Last updated from:ace54658ca. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK225
source / vignettesOK246
linux-release-x86_64OK220
macos-release-arm64OK185
macos-oldrel-arm64OK216
windows-develOK156
windows-releaseOK164
windows-oldrelOK145
wasm-releaseOK143

Exports:calculate_instability_metricsextract_allelesextract_fragmentsextract_ladder_summaryextract_repeat_correction_summaryextract_trace_tablefix_ladders_interactivegenemapper_table_to_fragmentsload_configplot_batch_correction_samplesplot_data_channelsplot_fragmentsplot_laddersplot_repeat_correction_modelplot_tracesread_fsaremove_fragmentsrepeat_table_to_fragmentssize_table_to_fragmentstrace

Dependencies:ade4askpassbase64encbootbslibcachemclicommonmarkcpp11crosstalkcurldata.tabledigestdplyrevaluatefarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixmemoisemgcvmimeminqanlmenloptropensslotelpillarpixmappkgconfigplotlypracmapromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownS7sassscalessegmentedseqinrshinysourcetoolsspstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml

Experimental considerations
Unique sample IDs | Index assignment and metrics | Fragment analysis batch effects | Ladders
Rendered fromexperimental_considerations.Rmdusingknitr::rmarkdown

Last update: 2025-12-23
Started: 2025-12-23

Plotting traces
Example data | plotting a trace | Extract raw traces | Join metadata | Plot the traces
Rendered fromplotting_traces.Rmdusingknitr::rmarkdown

Last update: 2025-12-23
Started: 2024-09-02

Readme and manuals

Help Manual

Help pageTopics
Calculate Repeat Instability Metricscalculate_instability_metrics
A list of fsa filescell_line_fsa_list
example_dataexample_data
example_data_repeat_tableexample_data_repeat_table
Extract Modal Peaksextract_alleles
Extract All Fragmentsextract_fragments
Extract ladder summaryextract_ladder_summary
Extract repeat correction summaryextract_repeat_correction_summary
Extract tracesextract_trace_table
Fix ladders interactivelyfix_ladders_interactive
fragments objectfragments
Convert Genemapper Peak Table to fragments classgenemapper_table_to_fragments
Load Trace Config Fileload_config
metadatametadata
Plot correction samplesplot_batch_correction_samples
plot_data_channelsplot_data_channels
Plot Peak Dataplot_fragments
Plot ladderplot_ladders
Plot Repeat Correction Modelplot_repeat_correction_model
Plot sample tracesplot_traces
Read fsa fileread_fsa
Remove Samples from Listremove_fragments
Convert Repeat Table to Repeats Fragmentsrepeat_table_to_fragments
Convert Size Table to Fragmentssize_table_to_fragments
Main function for sample processingtrace