transmogR
Bioc currentModify a set of reference sequences using a set of variants
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
16 7 exported
Complexity
6 avg / 28 max
Call network
16 nodes / 9 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
4,411
Files
74
Compiled share
7.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
14
Internal functions
6
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.31
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
5.6%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-06-30
Avg cadence
213 days
Cold removal rate
–
Dep drift
11
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
- 98%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Stevie Pederson author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("transmogR")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 v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.