MetaScope
Bioc currentTools and functions for preprocessing 16S and metagenomic sequencing microbiome data
Release Lineage
Entered 3.17 · Apr 26, 2023
Current · Requires R 4.6
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.
None published for Bioconductor
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 →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
7,540
Files
94
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
22
Internal functions
46
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
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
- Help pages
- 43 (5 internal)includes a package overview page
- Examples that run
- 70%16 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 4 never run
- Exported functions with examples
- 90%
- Documented parameters
- 98%
- Return-value docs
- 95%
- Help pages citing references
- 5%
Repository practices
3 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/wejlab/metascope on 2026-10-22.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| align_details | list | 6 elements | No other package |
| barcodes | data.frame | 6 × 2 | No other package |
| bowtie_target.filtered | data.frame | 5 × 6 | No other package |
| bt2_16S_params | vector | 1 element | No other package |
| bt2_missing_params | vector | 1 element | No other package |
| bt2_regular_params | vector | 1 element | No other package |
| subread_target.filtered | data.frame | 186 × 6 | No other package |
1 internal object is bundled for the package's own use and not listed here.
Topics
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")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 v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.