ExCluster
Bioc currentExCluster robustly detects differentially expressed exons between two conditions of RNA-seq data, requiring at least two independent biological replicates per condition
Release Lineage
Entered 3.8 · Oct 31, 2018
Current · Requires R 4.6
Description
ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 0 exported
Complexity
7.1 avg / 50 max
Call network
31 nodes / 31 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
2,774
Files
28
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
31
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
0%
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
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
16
First release
2019-01-04
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 5
- Examples that run
- 100%5 run in a plain check
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 80%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| normCounts | data.frame | 23 × 4 | No other package |
| sub_ExClust_results | data.frame | 19 × 16 | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("ExCluster")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.