tximeta
Bioc currentTranscript Quantification Import with Automatic Metadata
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
Transcript quantification import from Salmon and other quantifiers with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
56 16 exported
Complexity
4.7 avg / 19 max
Call network
56 nodes / 97 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
5,641
Files
52
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
16
Internal functions
40
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.17
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-01-11
Latest release
2026-04-28
Avg cadence
176 days
Cold removal rate
100%
Dep drift
11
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 16includes a package overview page
- Examples that run
- 92%11 run in a plain check · 1 never run
- Exported functions with examples
- 79%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 6%
- Updates to vignette to mention edgeR's new function
DGEListFromTximeta. - Fix the 'call dbDisconnect() when finished' message by explicitly doing it on exit. Thanks to Gordon Smyth for noting this.
From NEWS.md in the release
Repository practices
8 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/thelovelab/tximeta on 2026-10-22.
The R CMD check workflow runs on Linux and macOS, and on R-devel
GitHub Pages site last deployed 2026-07-20 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| hashtable | data.frame | 314 × 7 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
Suggested by (3)
People
- Michael Love author maintainer
- CZI funder
- NIH NHGRI funder
- Peter Hickey author contributor
- Rob Patro author contributor
- Charlotte Soneson author contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("tximeta")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1371/journal.pcbi.1007664.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.