NetActivity
Bioc currentCompute gene set scores from a deep learning framework
Release Lineage
Entered 3.16 · Nov 2, 2022
Current · Requires R 4.6
Description
#' NetActivity enables to compute gene set scores from previously trained sparsely-connected autoencoders. The package contains a function to prepare the data (`prepareSummarizedExperiment`) and a function to compute the gene set scores (`computeGeneSetScores`). The package `NetActivityData` contains different pre-trained models to be directly applied to the data. Alternatively, the users might use the package to compute gene set scores using custom models.
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
2 2 exported
Complexity
11 avg / 13 max
Call network
2 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
717
Files
19
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
2
Internal functions
0
Testing & CI
Has tests
Yes
Test-to-code ratio
0.85
testthat edition
3
CI present
No
CI type
[]
PR gated
No
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
4.1.0
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
8
First release
2022-11-01
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
- Examples that run
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- References docs
- 0%
Topics
People
- Carlos Ruiz-Arenas author maintainer
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("NetActivity")This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.
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