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NetActivity

This is the development version of NetActivity; for the stable release version, see NetActivity.

Compute gene set scores from a deep learning framework

Bioconductor version: Development (3.18)

#' 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 "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews FunctionalGenomics, GO, GeneExpression, Microarray, Pathways, RNASeq, Software, Transcription
Version 1.3.0
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
Linking To
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_1.3.0.tar.gz
Windows Binary NetActivity_1.3.0.zip (64-bit only)
macOS Binary (x86_64) NetActivity_1.3.0.tgz
macOS Binary (arm64)
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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