SurfR
Bioc currentSurface Protein Prediction and Identification
Release Lineage
Entered 3.19 · May 1, 2024
Current · Requires R 4.6
Description
Identify Surface Protein coding genes from a list of candidates. Systematically download data from GEO and TCGA or use your own data. Perform DGE on bulk RNAseq data. Perform Meta-analysis. Descriptive enrichment analysis and plots.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
22 18 exported
Complexity
5.6 avg / 14 max
Call network
22 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
3,795
Files
52
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
17
Internal functions
4
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.10
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
3
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.4.0
System requirements
–
C++ standard
–
License
GPL-3 + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
5
First release
2024-04-30
Latest release
2026-04-28
Avg cadence
188 days
Cold removal rate
–
Dep drift
4
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 25 (3 internal)
- Examples that run
- 12%2 run in a plain check · 15 never run
- Exported functions with examples
- 94%
- Documented parameters
- 96%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks run against github.com/auroramaurizio/surfr on 2026-10-21.
No development-tooling practices detected in the upstream repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| countData | matrix | 2,500 × 4 | No other package |
| enrichedList | list | 2 elements | No other package |
| ind_deg | list | 2 elements | No other package |
| metadata | data.frame | 4 × 3 | No other package |
Topics
People
- Aurora Maurizio author maintainer
- Anna Sofia Tascini author contributor
Cite
Cite this package
Run in R for the authors' entry:
citation("SurfR")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1093/bioadv/vbae201.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.