DOTSeq
Bioc currentGenome-wide Detection of Differential ORF Usage
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
Differential open reading frame (ORF) translation analysis framework for ribosome profiling (Ribo-seq) with matched RNA-seq. Implements (i) Differential ORF Usage (DOU), a beta-binomial generalized linear model that models the expected proportion of Ribo-seq versus RNA-seq reads mapping to each ORF within a gene, and (ii) ORF-level Differential Translation Efficiency (DTE), a negative binomial GLM that capture changes in translation efficiency of individual ORFs across experimental conditions. Supports ORF-level read summarization for bulk and single-cell Ribo-seq.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
81 14 exported
Complexity
8.8 avg / 78 max
Call network
81 nodes / 87 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
17,726
Files
126
Compiled share
2.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
24
Internal functions
53
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
CI present
No
CI type
[]
PR gated
No
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 58%
- Documented parameters
- 90%
- Return-value docs
- 94%
- References docs
- 34%
Topics
People
- Chun Shen Lim author maintainer
- Marsden fnd
- Gabrielle Chieng author contributor