PhosR
Bioc currentA set of methods and tools for comprehensive analysis of phosphoproteomics data
Release Lineage
Entered 3.12 · Oct 28, 2020
Current · Requires R 4.6
Description
PhosR is a package for the comprenhensive analysis of phosphoproteomic data. There are two major components to PhosR: processing and downstream analysis. PhosR consists of various processing tools for phosphoproteomics data including filtering, imputation, normalisation, and functional analysis for inferring active kinases and signalling pathways.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
53 32 exported
Complexity
4.5 avg / 19 max
Call network
53 nodes / 25 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
11,614
Files
101
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
44
Internal functions
21
Testing & CI
Has tests
Yes
Test-to-code ratio
0.12
testthat edition
–
CI present
Yes
CI type
["github-actions","travis"]
PR gated
Yes
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
4.2.0
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
12
First release
2020-10-27
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
13
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Examples that run
- 87%
- Documented parameters
- 96%
- Return-value docs
- 94%
- References docs
- 6%
Topics
Depended on by (1)
Bioconductor (1)
People
- Di Xiao author maintainer
- Hani Jieun Kim author
- Pengyi Yang author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("PhosR")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.