FRASER
Bioc currentFind RAre Splicing Events in RNA-Seq Data
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
325 60 exported
Complexity
4 avg / 28 max
Call network
325 nodes / 598 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
18,230
Files
105
Compiled share
4.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
90
Internal functions
211
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
–
Docs
Roxygen coverage
96.7%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
2.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
file LICENSE
License flags
SPDX valid, not OSI
History
Versions
13
First release
2020-09-04
Latest release
2026-04-28
Avg cadence
166 days
Cold removal rate
100%
Dep drift
5
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 25
- Examples that run
- 100%20 run in a plain check
- Exported functions with examples
- 95%
- Documented parameters
- 87%
- Return-value docs
- 95%
- Help pages citing references
- 0%
Repository practices
3 development-tooling and community-health practices detected across 2 families in the upstream repository
Checks run against github.com/gagneurlab/fraser on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| annotation | data.frame | 5 × 6 | No other package |
| hg19_NCBI2UCSC | data.frame | 360 × 4 | No other package |
| hg38_NCBI2UCSC | data.frame | 711 × 4 | No other package |
| k_j_counts | – | – | – |
| k_theta_counts | – | – | – |
| n_psi3_counts | – | – | – |
| n_psi5_counts | – | – | – |
| n_theta_counts | – | – | – |
| raw_junction_counts | – | – | – |
| raw_site_counts | – | – | – |
| sampleTable | data.frame | 3 × 5 | No other package |
| sampleTable_countTable | data.frame | 12 × 4 | No other package |
Topics
People
- Christian Mertes author maintainer
- Julien Gagneur author
- Ata Jadid Ahari contributor
- Karoline Lutz contributor
- Ines Scheller author
- Vicente Yepez author
Cite
Cite this package
Run in R for the authors' entry:
citation("FRASER")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/s41467-020-20573-7.
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.