PathoStat
Bioc currentPathoStat Statistical Microbiome Analysis Package
Release Lineage
Entered 3.4 · Oct 18, 2016
Current · Requires R 4.6
Description
The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 31 exported
Complexity
3.4 avg / 18 max
Call network
38 nodes / 13 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
2,445
Files
95
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
32
Internal functions
7
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
20
First release
2016-10-17
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
21
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 34
- Examples that run
- 100%32 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 97%
- Help pages citing references
- 0%
- PathoStat intro HTML
Repository practices
Checks run against github.com/mani2012/pathostat on 2026-10-11.
No development-tooling practices detected in the upstream repository.
Datasets
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("PathoStat")Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.