0.16.6 documentation

Complete canonical API text; task articles explain the workflows. Tutorials

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Setup and learning paths

HomeInstall and prepare the environmentChoose your learning module

Module I · Chord

1.1 Tables and field meanings1.2 Produce and import comparisons1.3 Build the layers step by step1.4 Direction, curvature and clearance1.5 Filter and summarize links1.6 Full source-file workflow1.7 Complete chord showcase

Module II · Collinear

2.1 Reuse chord input tables2.2 Switch coordinates and add layers2.3 Routes, clearance and the ruler2.4 Compare CDS neighbourhoods2.5 Focus, anchors and segments2.6 Complete collinear showcase

Module III · Plasmid

3.1 DNA, annotations and 13 references3.2 From a circle to annotation layers3.3 Features, primers and restriction3.4 Thirteen plasmid references3.5 Complete plasmid cases

Consult as needed · Data and layers

Prepare tables and coordinatesImport and convert dataImport nucleotide and protein alignmentsProject protein intervals to genomic coordinatesFeatures, stacking and genomic decorationLabels and local placementQuantitative tracksMappings, scales, guides and themesSet values by sequence and strandCommon adjustments and grammarExport, preview and diagnostics

Learning map and reference

Articles and complete workflowsFunction referenceReproducible galleryFrequently asked questionsMigrate to the candidate APITerminology and design sourcesDevelopment status and changes

Inspect the bundled sequencing-primer catalogue

On this page

• Usage
• Arguments
• Value
• See also
• Examples

The catalogue stores one searchable record per distinct oligonucleotide. Set aliases = TRUE to obtain the source rows, including multiple biological names that share one sequence. The source direction is retained only as a descriptive hint; binding strand is determined from the target sequence.

Usage

Code

primer_catalog(set = c("all", "universal"), aliases = FALSE)

Arguments

set

Return all records or only the commonly used universal subset.

aliases

Return source alias records instead of the sequence catalogue.

Value

A data frame.

See also

ggchord_data_contract

Examples

Code

head(primer_catalog("universal"))
head(primer_catalog("universal", aliases = TRUE))