NetActivity
Compute gene set scores from a deep learning framework
Bioconductor version: Release (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("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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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/ |
| Package Downloads Report | Download Stats |