sangeranalyseR
Bioc currentsangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
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.
None published for Bioconductor
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
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
15,711
Files
446
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
98
Testing
Has tests
Yes
Test-to-code ratio
0.13
testthat edition
–
Docs
Roxygen coverage
85.7%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
7.4%
Secret pattern count
0
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
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 46
- Examples that run
- 100%41 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- sangeranalyseR HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| TRACE_FILE_INFO | data.frame | 10 × 5 | No other package |
| names_conversion | data.frame | 8 × 3 | No other package |
| names_conversion_1 | data.frame | 2 × 3 | No other package |
| names_conversion_2 | data.frame | 2 × 3 | No other package |
| names_conversion_all | data.frame | 16 × 3 | No other package |
| qualityReportData | – | – | – |
| sangerAlignmentData | – | – | – |
| sangerContigData | – | – | – |
| sangerReadFData | – | – | – |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("sangeranalyseR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/gbe/evab028.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.