DuplexDiscovereR
Bioc currentAnalysis of the data from RNA duplex probing experiments
Release Lineage
Entered 3.20 · Oct 30, 2024
Current · Requires R 4.6
Description
DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
53 22 exported
Complexity
3.2 avg / 12 max
Call network
53 nodes / 67 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
7,894
Files
98
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
27
Internal functions
31
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.06
testthat edition
3
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
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.5
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
4
First release
2024-10-29
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
2
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
- 99%
- Return-value docs
- 96%
- References docs
- 0%
Datasets
| Name | Class | Rows × Cols | Also in |
|---|---|---|---|
| RNADuplexSampleClustReads | – | – | – |
| RNADuplexSampleDGs | – | – | – |
| RNADuplexSampleGI | – | – | – |
| RNADuplexesGeneCounts | spec_tbl_df | 1,445 × 2 | No other package |
| RNADuplexesRawBed | spec_tbl_df | 2,040 × 10 | No other package |
| RNADuplexesRawChimSTAR | tibble | 5,000 × 21 | No other package |
| SampleGeneAnnoGR | – | – | – |
| SampleSmallGI | – | – | – |
| SampleSpliceJncGR | – | – | – |
| test_geneCounts | data.frame | 1,445 × 2 | No other package |
Topics
People
- Egor Semenchenko author maintainer cph
- Irmtraud M. Meyer author cph
- Volodymyr Tsybulskyi contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("DuplexDiscovereR")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.