fluentGenomics
Bioc currentA plyranges and tximeta workflow
Release Lineage
Entered 3.11 · Apr 28, 2020
Current · Requires R 4.6
Description
An extended workflow using the plyranges and tximeta packages for fluent genomic data analysis. Use tximeta to correctly import RNA-seq transcript quantifications and summarize them to gene counts for downstream analysis. Use plyranges for clearly expressing operations over genomic coordinates and to combine results from differential expression and differential accessibility analyses.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
5 1 exported
Complexity
1.8 avg / 3 max
Call network
5 nodes / 4 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
1,298
Files
13
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
1
Internal functions
4
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
16.7%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
13
First release
2020-05-22
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
- 2
- Examples that run
- 100%1 run in a plain check (under a condition)
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- fluentGenomics HTML
Repository practices
7 development-tooling and community-health practices detected across 4 families in the upstream repository
Checks run against github.com/sa-lee/fluentgenomics on 2026-10-21.
The R CMD check workflow runs on Linux and macOS, and on R-devel
GitHub Pages site last deployed 2026-06-10 · The repository has a site deploy workflow
Datasets
Topics
People
- Stuart Lee author maintainer
- Michael Love author contributor
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("fluentGenomics")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
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.