topdownr
Bioc currentInvestigation of Fragmentation Conditions in Top-Down Proteomics
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
134 10 exported
Complexity
3.1 avg / 14 max
Call network
134 nodes / 150 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
10,397
Files
78
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
11
Internal functions
124
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.52
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
60%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
3
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
- 96%
- Return-value docs
- 86%
- References docs
- 15%
Topics
Depended on by (1)
Bioconductor (1)
People
- Sebastian Gibb author maintainer
- Ole Nørregaard Jensen author
- Pavel Shliaha author