IsoformSwitchAnalyzeR
Bioc currentIdentify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNA-seq (short/long) by tools such as Kallisto, Salmon, StringTie, Tallon, IsoQuant etc.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
92 0 exported
Complexity
26 avg / 263 max
Call network
92 nodes / 137 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
36,742
Files
102
Compiled share
0.2%
Has compiled src
Yes
Language breakdown
API
Exported functions
52
Internal functions
88
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
11.9%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.2
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
26
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 50
- Examples that run
- 98%45 run in a plain check · 1 never run
- Exported functions with examples
- not tracked
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 98%
Repository practices
2 development-tooling and community-health practices detected across 1 family in the upstream repository
Checks run against github.com/kvittingseerup/isoformswitchanalyzer on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| cpat_results | data.frame | 490 × 8 | No other package |
| cpc2_result | data.frame | 161 × 7 | No other package |
| deeploc2 | data.frame | 160 × 13 | No other package |
| exampleSwitchList | switchAnalyzeRlist | 10 elements | No other package |
| exampleSwitchListAnalyzed | switchAnalyzeRlist | 13 elements | No other package |
| exampleSwitchListIntermediary | switchAnalyzeRlist | 10 elements | No other package |
| iupred2a_result | – | – | – |
| netsurfp3_result | data.frame | 79,651 × 21 | No other package |
| pfam_results | – | – | – |
| signalP_results | – | – | – |
Topics
People
- Kristoffer Vitting-Seerup maintainer author
- Elena Iriondo Delgado contributor
- Jeroen Gilis contributor
- Chunxu Han contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("IsoformSwitchAnalyzeR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1158/1541-7786.mcr-16-0459, 10.1093/bioinformatics/btz247.
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.