tradeSeq
Bioc currenttrajectory-based differential expression analysis for sequencing data
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
tradeSeq provides a flexible method for fitting regression models that can be used to find genes that are differentially expressed along one or multiple lineages in a trajectory. Based on the fitted models, it uses a variety of tests suited to answer different questions of interest, e.g. the discovery of genes for which expression is associated with pseudotime, or which are differentially expressed (in a specific region) along the trajectory. It fits a negative binomial generalized additive model (GAM) for each gene, and performs inference on the parameters of the GAM.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
40 3 exported
Complexity
12.5 avg / 36 max
Call network
40 nodes / 61 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
8,377
Files
70
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
37
Testing
Has tests
Yes
Test-to-code ratio
0.22
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
3.6
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2020-04-03
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
13
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 22
- Examples that run
- 94%16 run in a plain check · 1 never run
- Exported functions with examples
- 100%
- Documented parameters
- 94%
- Return-value docs
- 94%
- Help pages citing references
- 5%
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/statomics/tradeseq on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2021-03-30 · The repository has a site deploy workflow
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| celltype | vector | 2,660 elements | No other package |
| countMatrix | dgCMatrix | 240 × 2,660 | No other package |
| crv | – | – | – |
| gamList | list | 11 elements | No other package |
| sds | – | – | – |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (2)
People
- Hector Roux de Bezieux author maintainer
- Lieven Clement author contributor
- Sandrine Dudoit contributor
- Kelly Street author contributor
- Koen Van den Berge author
Cite
Cite this package
Run in R for the authors' entry:
citation("tradeSeq")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.