HMP2Data
Bioc current16s rRNA sequencing data from the Human Microbiome Project 2
Release Lineage
Entered 3.10 · Oct 30, 2019
Current · Requires R 4.6
Description
HMP2Data is a Bioconductor package of the Human Microbiome Project 2 (HMP2) 16S rRNA sequencing data. Processed data is provided as phyloseq, SummarizedExperiment, and MultiAssayExperiment class objects. Individual matrices and data.frames used for building these S4 class objects are also provided in the package.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
11 8 exported
Complexity
2.5 avg / 4 max
Call network
11 nodes / 0 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
1,587
Files
57
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
8
Internal functions
3
Testing
Has tests
Yes
Test-to-code ratio
0.03
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.6.0
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
14
First release
2019-10-29
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 19
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 0%
- HMP2Data HTML
Repository practices
Checks run against github.com/jstansfield0/hmp2data on 2026-10-22.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| IBD16S_mtx | matrix | 982 × 178 | No other package |
| IBD16S_samp | data.frame | 178 × 490 | No other package |
| IBD16S_tax | matrix | 982 × 6 | No other package |
| T2D16S_mtx | matrix | 12,062 × 2,208 | No other package |
| T2D16S_samp | data.frame | 2,208 × 13 | No other package |
| T2D16S_tax | matrix | 12,062 × 7 | No other package |
| momspi16S_mtx | matrix | 7,665 × 9,107 | No other package |
| momspi16S_samp | data.frame | 9,107 × 13 | No other package |
| momspi16S_tax | matrix | 7,665 × 7 | No other package |
| momspiCyto_mtx | matrix | 29 × 1,396 | No other package |
| momspiCyto_samp | data.frame | 1,396 × 13 | No other package |
Topics
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("HMP2Data")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.