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 (3.23)

#' 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 "4.6") 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


Reference Manual	PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	FunctionalGenomics, GO, GeneExpression, Microarray, Pathways, RNASeq, Software, Transcription
Version	1.13.0
In Bioconductor since	BioC 3.16 (R-4.2) (3 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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Build Report	Build Report

Package Archives

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

Source Package
Windows Binary (x86_64)
macOS Binary (x86_64)
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
Package Short Url	https://bioconductor.org/packages/NetActivity/
Package Downloads Report	Download Stats