easyRNASeq
Bioc currentCount summarization and normalization for RNA-Seq data
Release Lineage
Entered 2.10 · Apr 2, 2012
Current · Requires R 4.6
Description
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
31 2 exported
Complexity
3.8 avg / 21 max
Call network
31 nodes / 11 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
10,582
Files
109
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
13
Internal functions
1
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
92.3%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
39
Dep constraint coverage
77.3%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
–
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
29
First release
2012-08-26
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
14
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 41 (6 internal)includes a package overview page
- Examples that run
- 66%19 run in a plain check · 9 never run · 1 hold no code
- Exported functions with examples
- 67%
- Documented parameters
- 100%
- Return-value docs
- 33%
- Help pages citing references
- 0%
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 |
|---|---|---|---|
| RobinsonDelhomme2014 | data.frame | 17 × 7 | No other package |
Topics
Depended on by (2)
Bioconductor (2)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("easyRNASeq")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioinformatics/bts477.
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.