basecallQC
Bioc currentWorking with Illumina Basecalling and Demultiplexing input and output files
Release Lineage
Entered 3.5 · Apr 25, 2017
Current · Requires R 4.6
Description
The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
48 11 exported
Complexity
2.7 avg / 16 max
Call network
48 nodes / 20 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
3,267
Files
79
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
19
Internal functions
36
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.21
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.4
System requirements
1
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
19
First release
2017-06-08
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
Thomas Carroll
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("basecallQC")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.