specL
Bioc currentspecL - Prepare Peptide Spectrum Matches for Use in Targeted Proteomics
Release Lineage
Entered 3.0 · Oct 14, 2014
Current · Requires R 4.6
Description
provides a functions for generating spectra libraries that can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software. The package is developed, tested and used at the Functional Genomics Center Zurich <https://fgcz.ch>.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
21 7 exported
Complexity
2.8 avg / 15 max
Call network
21 nodes / 2 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
3,445
Files
44
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
14
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
24
First release
2014-10-13
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 12
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 88%
- Return-value docs
- 100%
- Help pages citing references
- 17%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/fgcz/specl on 2026-10-21.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| iRTpeptides | data.frame | 31 × 2 | 2 packages |
| ms1.p2069 | vector | 11,830 elements | No other package |
| peptideStd | psmSet | 137 elements | No other package |
| peptideStd.redundant | psmSet | 184 elements | No other package |
Topics
Suggested by (2)
People
- Christian Panse author maintainer
- Jonas Grossmann author
- Christian Trachsel author
- Witold E. Wolski contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("specL")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.