BANDITS
Bioc currentBANDITS: Bayesian ANalysis of DIfferenTial Splicing
Release Lineage
Entered 3.9 · May 3, 2019
Current · Requires R 4.6
Description
BANDITS is a Bayesian hierarchical model for detecting differential splicing of genes and transcripts, via differential transcript usage (DTU), between two or more conditions. The method uses a Bayesian hierarchical framework, which allows for sample specific proportions in a Dirichlet-Multinomial model, and samples the allocation of fragments to the transcripts. Parameters are inferred via Markov chain Monte Carlo (MCMC) techniques and a DTU test is performed via a multivariate Wald test on the posterior densities for the average relative abundance of transcripts.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
77 7 exported
Complexity
6 avg / 37 max
Call network
77 nodes / 53 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
7,776
Files
83
Compiled share
26.6%
Has compiled src
Yes
Language breakdown
API
Exported functions
7
Internal functions
38
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
1 externalC++17
C++ standard
C++17
License
GPL (>= 3)
License flags
SPDX valid, OSI approved
History
Versions
15
First release
2019-05-02
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 14includes a package overview page
- Examples that run
- 100%13 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/simonetiberi/bandits on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| gene_tr_id | data.frame | 1,373 × 2 | No other package |
| input_data | – | – | – |
| precision | list | 2 elements | No other package |
| pseudoalignments | data.frame | 4,718 × 2 | No other package |
| results | – | – | – |
Topics
Depended on by (1)
Bioconductor (1)
People (from the free-text Author field)
- Simone Tiberi. author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("BANDITS")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1186/s13059-020-01967-8.
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.