tximport
Bioc currentImport and summarize transcript-level estimates for transcript- and gene-level analysis
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
18 2 exported
Complexity
9.3 avg / 80 max
Call network
18 nodes / 17 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
2,828
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
3
Internal functions
16
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.20
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
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
LGPL (>=2)
License flags
not SPDX, not OSI
History
Versions
21
First release
2016-06-17
Latest release
2026-04-28
Avg cadence
182 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
- Help pages
- 4includes a package overview page
- Examples that run
- 100%1 run in a plain check
- Exported functions with examples
- 33%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 50%
- Updates from Gordon Smyth and Pedro Baldoni to the vignette using new functions in edgeR.
From NEWS in the release
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/thelovelab/tximport on 2026-10-18.
Topics
Depended on by (13)
Show all 18 packagesHide all 18 packages
Bioconductor (11)
Suggested by (5)
People (from the free-text Author field)
- Michael Love maintainer author
- Charlotte Soneson author
- Mark Robinson author
- Rob Patro contributor
- Andrew Parker Morgan contributor
- Ryan C. Thompson contributor
- Matt Shirley contributor
- Avi Srivastava contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("tximport")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.12688/f1000research.7563.1.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.