CrcBiomeScreen
Bioc currentAn R package for colorectal cancer screening and microbiome analysis
Release Lineage
Entered 3.23 · Apr 29, 2026
Current · Requires R 4.6
Description
A developed and benchmarked reproducible machine learning framework for microbiome-based colorectal cancer (CRC) screening. By systematically evaluating normalization strategies, taxonomic resolutions, and class imbalance handling. This R package allows users to apply the full pipeline or selectively run specific components depending on their analytical needs. It establishes a scalable foundation for developing interpretable microbiome-based screening tools to support early CRC detection. This approach could be easily implemented in a national screening programme, to improve early detection rates for this disease.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 22 exported
Complexity
5.1 avg / 20 max
Call network
22 nodes / 12 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
6,328
Files
79
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
34
Internal functions
0
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.10
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
100%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2026-04-28
Latest release
2026-04-28
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 38
- Examples that run
- 94%32 run in a plain check · 2 hold no code
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- CrcBiomeScreen HTML
Repository practices
Checks run against github.com/omicsforestry/crcbiomescreen on 2026-10-18.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| NHSBCSP_screeningData | data.frame | 2,252 × 647 | No other package |
| Thomas_2018_RelativeAbundance | list | 1 element | No other package |
| ZellerG_2014_RelativeAbundance | list | 1 element | No other package |
Topics
People
- Chengxin Li maintainer author
- Rishabh Bezbaruah author
- Arief Gusnanto author
- Henry Wood author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("CrcBiomeScreen")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 v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.