NetActivity
This is the development version of NetActivity; for the stable release version, see NetActivity.
All Bioconductor versions of NetActivity
3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16
Compute gene set scores from a deep learning framework
Bioconductor version: 3.24 · Package version: 1.15.0
#' 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.
Author: Carlos Ruiz-Arenas [aut, cre]
Maintainer: Carlos Ruiz-Arenas <carlos.ruiza at upf.edu>
Citation
From within R, enter citation("NetActivity"):
Carlos Ruiz-Arenas. NetActivity: Compute gene set scores from a deep learning framework. doi:10.18129/B9.bioc.NetActivity, R package version 1.15.0, https://bioconductor.org/packages/NetActivity.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("NetActivity")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.15.0 |
| License | MIT + file LICENSE |
| Last updated | 2026-04-28 |
| In Bioconductor since | BioC 3.16 (R-4.2) (3 years) |
| Downloads rank | 1805 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | FunctionalGenomics, GO, GeneExpression, Microarray, Pathways, RNASeq, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/NetActivity/ |
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("NetActivity")| Gene set scores computation with NetActivity | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | NetActivity_1.15.0.tar.gz |
| Windows binary (x86_64) | NetActivity_1.15.0.zip |
| macOS binary (arm64) | NetActivity_1.15.0.tgz |
| macOS binary (x86_64) | NetActivity_1.15.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/NetActivity |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/NetActivity |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.1.0)
Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils
Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse