Rmmquant
Bioc currentRNA-Seq multi-mapping Reads Quantification Tool
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
34 3 exported
Complexity
2.1 avg / 9 max
Call network
34 nodes / 22 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
3,447
Files
34
Compiled share
61.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
4
Internal functions
4
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.97
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
8.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
1
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-02-27
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
1
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
- Zytnicki Matthias author maintainer