Package: trace 0.5.0
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:
trace_0.5.0.tar.gz
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trace.pdf |trace.html✨
trace/json (API)
NEWS
| # 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 site:https://zachariahmclean.github.io
- cell_line_fsa_list - A list of fsa files
- example_data - Example_data
- example_data_repeat_table - Example_data_repeat_table
- metadata - Metadata
Last updated 1 months agofrom:2303a29b7a. Checks:7 OK, 1 ERROR. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 16 2025 |
| R-4.5-win | OK | Feb 16 2025 |
| R-4.5-mac | OK | Feb 16 2025 |
| R-4.5-linux | OK | Feb 16 2025 |
| R-4.4-win | OK | Feb 18 2025 |
| R-4.4-mac | OK | Feb 16 2025 |
| R-4.3-win | OK | Feb 16 2025 |
| R-4.3-mac | ERROR | Feb 18 2025 |
Exports:add_metadataassign_index_peakscalculate_instability_metricscall_repeatsextract_allelesextract_fragmentsextract_ladder_summaryextract_repeat_correction_summaryextract_trace_tablefind_allelesfind_fragmentsfind_laddersfix_ladders_interactivefix_ladders_manualgenerate_trace_templatepeak_table_to_fragmentsplot_batch_correction_samplesplot_data_channelsplot_fragmentsplot_laddersplot_repeat_correction_modelplot_tracesread_fsaremove_fragmentsrepeat_table_to_repeats
Dependencies:ade4askpassbase64encbootbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrMASSMatrixmemoisemgcvmimeminqamunsellnlmenloptropensslpillarpixmappkgconfigplotlypracmapromisespurrrR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreformulasrlangrmarkdownsassscalessegmentedseqinrshinysourcetoolsspstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunxtableyaml
