Modstrings
Bioc currentWorking with modified nucleotide sequences
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
Representing nucleotide modifications in a nucleotide sequence is usually done via special characters from a number of sources. This represents a challenge to work with in R and the Biostrings package. The Modstrings package implements this functionallity for RNA and DNA sequences containing modified nucleotides by translating the character internally in order to work with the infrastructure of the Biostrings package. For this the ModRNAString and ModDNAString classes and derivates and functions to construct and modify these objects despite the encoding issues are implemenented. In addition the conversion from sequences to list like location information (and the reverse operation) is implemented as well.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
106 17 exported
Complexity
2.7 avg / 11 max
Call network
106 nodes / 94 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
7,412
Files
72
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
28
Internal functions
88
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.28
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
9.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-06-25
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
- Help pages
- 18 (1 internal)includes a package overview page
- Examples that run
- 100%14 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 78%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- Modstrings-DNA-alphabet HTML
- Modstrings-RNA-alphabet HTML
- Modstrings HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/felixernst/modstrings on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2025-12-24 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| DNAmod_modifications | data.frame | 47 × 4 | No other package |
| MOD_RNA_DICT_MODOMICS | – | – | – |
| MOD_RNA_DICT_TRNADB | – | – | – |
| Mod_DNA_codes | data.frame | 47 × 7 | No other package |
| Mod_RNA_codes | – | – | – |
| modomics_modifications | data.frame | 168 × 3 | No other package |
| modsDNA | – | – | – |
| modsRNA | – | – | – |
| tRNAdb_modifications | data.frame | 58 × 3 | No other package |
Topics
Depended on by (4)
Bioconductor (4)
Suggested by (2)
People
- Felix G.M. Ernst author maintainer
- Denis L.J. Lafontaine contributor funder
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("Modstrings")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.