PhIPData
Bioc currentContainer for PhIP-Seq Experiments
Release Lineage
Entered 3.13 · May 20, 2021
Current · Requires R 4.6
Description
PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
28 13 exported
Complexity
3.2 avg / 10 max
Call network
28 nodes / 16 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
3,123
Files
35
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
21
Internal functions
15
Testing
Has tests
Yes
Test-to-code ratio
0.38
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
11
First release
2021-05-19
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
100%
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 8
- Examples that run
- 100%8 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 97%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
5 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/athchen/phipdata on 2026-10-21.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
Datasets
Topics
Depended on by (1)
Bioconductor (1)
People
- Athena Chen author maintainer
- Ingo Ruczinski author
- Rob Scharpf author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("PhIPData")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.