sangeranalyseR

Bioc current

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

v1.22.0 · software · GPL-2

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.12 · Oct 28, 2020

Current · Requires R 4.6

1.0 In 12 of 49 releases 3.23

Description

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

105 7 exported

Complexity

5.1 avg / 151 max

Call network

105 nodes / 94 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

15,711

Files

447

Compiled share

Has compiled src

Language breakdown

R 11,547 (73.5%)Tests 1,460 (9.3%)Docs 2,078 (13.2%)Vignettes 626 (4%)

API

Exported functions

Internal functions

Testing & CI

Has tests

Yes

Test-to-code ratio

0.13

testthat edition

–

CI present

Yes

CI type

["travis"]

PR gated

Docs

Roxygen coverage

85.7%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

Unsafe pattern score

Dep constraint coverage

7.4%

Secret pattern count

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.0.0

System requirements

–

C++ standard

–

License

GPL-2

License flags

SPDX valid, OSI approved

History

Versions

First release

2020-10-27

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

–

Dep drift

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 0% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 96%
Return-value docs: 100%
References docs: 0%

Topics

Software › ResearchField › Genetics

Software › WorkflowStep › Alignment

Software › Technology › Sequencing

Software › Technology › Sequencing › SangerSeq

Software › WorkflowStep › Preprocessing

Software › WorkflowStep › QualityControl

Software › WorkflowStep › Visualization

Software › Infrastructure › GUI

People

Kuan-Hao Chao

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