NetActivity

DOI: 10.18129/B9.bioc.NetActivity  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see NetActivity.

Compute gene set scores from a deep learning framework

Bioconductor version: 3.17

#' 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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	Gene set scores computation with NetActivity
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	FunctionalGenomics, GO, GeneExpression, Microarray, Pathways, RNASeq, Software, Transcription
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
License	MIT + file LICENSE
Depends	R (>= 4.1.0)
Imports	airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils
LinkingTo
Suggests	AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	NetActivity_1.2.0.tar.gz
Windows Binary	NetActivity_1.2.0.zip
macOS Binary (x86_64)	NetActivity_1.2.0.tgz
macOS Binary (arm64)	NetActivity_1.2.0.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/
Package Downloads Report	Download Stats