puma
Bioc currentPropagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0)
Release Lineage
Entered 2.0 · Apr 26, 2007
Current · Requires R 4.6
Description
Most analyses of Affymetrix GeneChip data (including tranditional 3' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
262 0 exported
Complexity
10.6 avg / 75 max
Call network
262 nodes / 215 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
30,731
Files
192
Compiled share
50.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
42
Internal functions
0
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
–
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
9
Dep constraint coverage
25%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.2.0
System requirements
–
C++ standard
–
License
LGPL
License flags
not SPDX, not OSI
History
Versions
39
First release
2007-08-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 61includes a package overview page
- Examples that run
- 79%33 run in a plain check · 9 hold no code
- Exported functions with examples
- 83%
- Documented parameters
- not tracked
- Return-value docs
- not tracked
- Help pages citing references
- 28%
Also includes 1 demo script (run with demo())
- puma User Guide PDF
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| Clust.exampleE | matrix | 700 × 20 | No other package |
| Clust.exampleStd | matrix | 700 × 20 | No other package |
| Clustii.exampleE | data.frame | 600 × 80 | No other package |
| Clustii.exampleStd | data.frame | 600 × 80 | No other package |
| eset_mmgmos | – | – | – |
| exampleE | matrix | 200 × 6 | No other package |
| exampleStd | matrix | 200 × 6 | No other package |
| hgu95aphis | vector | 3 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
Suggested by (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("puma")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.