bambu
Bioc currentContext-Aware Transcript Quantification from Long Read RNA-Seq data
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
168 9 exported
Complexity
2.7 avg / 17 max
Call network
168 nodes / 196 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
7,593
Files
154
Compiled share
2.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
9
Internal functions
153
Testing & CI
Has tests
Yes
Test-to-code ratio
0.19
testthat edition
–
CI present
Yes
CI type
["github-actions"]
PR gated
Yes
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
11.1%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2021-04-27
Latest release
2026-04-28
Avg cadence
177 days
Cold removal rate
–
Dep drift
4
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
- 100%
- Return-value docs
- 89%
- References docs
- 0%
Topics
Depended on by (2)
Bioconductor (2)
People
- Ying Chen maintainer author
- Jonathan Goeke author
- Andre Sim author
- Yuk Kei Wan author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("bambu")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.