NetActivity

This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see NetActivity.

Compute gene set scores from a deep learning framework

Bioconductor version: 3.19

#' 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")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("NetActivity")

For older versions of R, please refer to the appropriate Bioconductor release.

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 PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews FunctionalGenomics, GO, GeneExpression, Microarray, Pathways, RNASeq, Software, Transcription

Version 1.6.0

In Bioconductor since BioC 3.16 (R-4.2) (2 years)

License MIT + file LICENSE

Depends R (>= 4.1.0)

Imports airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils

System Requirements

URL

Suggests AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package NetActivity_1.6.0.tar.gz

Windows Binary (x86_64) NetActivity_1.6.0.zip

macOS Binary (x86_64) NetActivity_1.6.0.tgz

macOS Binary (arm64) NetActivity_1.6.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/NetActivity

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NetActivity

Bioc Package Browser https://code.bioconductor.org/browse/NetActivity/

Package Short Url https://bioconductor.org/packages/NetActivity/

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