srnadiff
Bioc currentFinding differentially expressed unannotated genomic regions from RNA-seq data
Release Lineage
Entered 3.7 · May 1, 2018
Current · Requires R 4.6
Description
srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
63 5 exported
Complexity
7.2 avg / 60 max
Call network
63 nodes / 48 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
5,014
Files
64
Compiled share
13.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
6
Internal functions
22
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.08
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
5.3%
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
17
First release
2018-04-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
12
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
- 83%
- References docs
- 20%
Topics
People
- Zytnicki Matthias author maintainer
- Gonzalez Ignacio author