topconfects
Bioc currentTop Confident Effect Sizes
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Rank results by confident effect sizes, while maintaining False Discovery Rate and False Coverage-statement Rate control. Topconfects is an alternative presentation of TREAT results with improved usability, eliminating p-values and instead providing confidence bounds. The main application is differential gene expression analysis, providing genes ranked in order of confident log2 fold change, but it can be applied to any collection of effect sizes with associated standard errors.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
16 9 exported
Complexity
4.4 avg / 16 max
Call network
16 nodes / 13 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
2,131
Files
34
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
9
Internal functions
7
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.11
testthat edition
–
CI present
Yes
CI type
["travis"]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
LGPL-2.1 | file LICENSE
License flags
SPDX valid, not OSI
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
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
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
Depended on by (3)
Bioconductor (3)
People
- Paul Harrison author maintainer