R Observatory: Metrics for MetaScope version 2.0.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MetaScope

Bioc current

Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

v2.0.0 · experiment · GPL (>= 3)

View on Bioconductor ↗ Source ↗

Release Lineage

Entered 3.17 · Apr 26, 2023

Current · Requires R 4.6

1.0 In 7 of 49 releases 3.23

Description

This package contains tools and methods for preprocessing microbiome data. Functionality includes library generation, demultiplexing, alignment, and microbe identification. It is in part an R translation of the PathoScope 2.0 pipeline.

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

69 22 exported

Complexity

4.8 avg / 31 max

Call network

69 nodes / 50 edges

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

Call graph

Open call graph →

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Lowest coverage

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

Code

Structure

Lines of code

7,540

Files

107

Compiled share

0%

Has compiled src

No

Language breakdown

R 4,473 (59.3%)Tests 3 (0%)Docs 2,440 (32.4%)Vignettes 624 (8.3%)

API

Exported functions

22

Internal functions

46

Recent export changes

v3.23+3 metascope_inspect, metascope_inspect_usage, run_metascope

v3.22+3 blast_reassignment, download_refseq_16S, metascope_blast

Testing & CI

Has tests

Yes

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Roxygen coverage

95.5%

Health & Security signals

Informational signals; not verdicts.

on.exit coverage

0%

Unsafe pattern score

2

Dep constraint coverage

5%

Secret pattern count

0

Bundled 3rd-party code

2 items

Portability & License

Min R version

4.2.0

System requirements

–

C++ standard

–

License

GPL (>= 3)

License flags

SPDX valid, OSI approved

History

Versions

7

First release

2023-04-25

Latest release

2026-04-28

Avg cadence

182 days

Cold removal rate

100%

Dep drift

6

LOC over versions

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

Documentation

READMEYes · 200 wordsVignettesYes · dynamicpkgdown siteYesNEWSYes · 67% structuredCode of conductYesContributing guideNo

Examples that run: 83%
Documented parameters: 98%
Return-value docs: 95%
References docs: 5%

Topics

ExperimentData › TechnologyData › SequencingData › MicrobiomeData

ExperimentData › ReproducibleResearch

ExperimentData › TechnologyData › SequencingData

People

Sean Lu author maintainer
W. Evan Johnson author
Aubrey Odom author
Rahul Varki author

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MetaScope")

Format

Lu, S., Johnson, W. E., Odom, A., & Varki, R. (2026). MetaScope: Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data (Version 2.0.0) [Computer software]. https://bioconductor.org/packages/MetaScope

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 MetaScope version 2.0.0 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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