R Observatory: Metrics for FLAMES version 2.6.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

FLAMES

Bioc current

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

v2.6.0 · software · GPL (>= 3)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.14 · Oct 27, 2021

Current · Requires R 4.6

1.0 In 10 of 49 releases 3.23

Description

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

658 43 exported

Complexity

5.7 avg / 34 max

Call network

658 nodes / 734 edges

Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

35,034

Files

268

Compiled share

63.6%

Has compiled src

Yes

Language breakdown

R 8,114 (23.2%)C/C++/src 22,285 (63.6%)Tests 853 (2.4%)Docs 3,431 (9.8%)Vignettes 351 (1%)

API

Exported functions

56

Internal functions

62

Recent export changes

v3.23+3 barcode_group, barcode_segment, find_diversity −1 sc_gene_entropy

v3.22+21 config<-, controllers<-, steps<- +18 more −6 find_isoform, get_GRangesList, minimap2_align 3 more

Testing & CI

Has tests

Yes

Test-to-code ratio

0.11

testthat edition

3

CI present

Yes

CI type

["github-actions"]

PR gated

Yes

Docs

Roxygen coverage

100%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

2

Dep constraint coverage

2%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2.0

System requirements

2

C++ standard

C++17

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

10

First release

2021-11-04

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

55

LOC over versions

Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.

Documentation

READMEYes · 380 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 67% structuredCode of conductYesContributing guideYes

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Topics

Software › Technology › Sequencing › RNASeq

Software › Technology › SingleCell

Software › ResearchField › Transcriptomics

Software › Infrastructure › DataImport

Software › BiologicalQuestion › DifferentialSplicing

Software › BiologicalQuestion › AlternativeSplicing

Software › AssayDomain › GeneExpression

Software › Technology › Sequencing › LongRead

People

Changqing Wang author maintainer
Yair D.J. Prawer author
Matthew Ritchie contributor
Jakob Schuster author
Shian Su author
Luyi Tian author
Oliver Voogd author
Yupei You author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("FLAMES")

Format

Wang, C., Prawer, Y. D. J., Ritchie, M., Schuster, J., Su, S., Tian, L., Voogd, O., & You, Y. (2026). FLAMES: FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data (Version 2.6.0) [Computer software]. https://bioconductor.org/packages/FLAMES

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for FLAMES version 2.6.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →