NetActivity

DOI: 10.18129/B9.bioc.NetActivity    

Compute gene set scores from a deep learning framework

Bioconductor version: Release (3.16)

#' 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 "4.2") 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 1.0.0
In Bioconductor since BioC 3.16 (R-4.2) (< 6 months)
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_1.0.0.tar.gz
Windows Binary NetActivity_1.0.0.zip
macOS Binary (x86_64) NetActivity_1.0.0.tgz
macOS Binary (arm64) NetActivity_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/NetActivity
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/NetActivity
Package Short Url https://bioconductor.org/packages/NetActivity/
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