NetActivity
Compute gene set scores from a deep learning framework
Bioconductor version: 3.23 · Package version: 1.14.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
#' 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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("NetActivity")Details
| Maintainer | Carlos Ruiz-Arenas <carlos.ruiza@upf.edu> |
| Author | Carlos Ruiz-Arenas [aut, cre] |
| License | MIT + file LICENSE |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | FunctionalGenomics, GO, GeneExpression, Microarray, Pathways, RNASeq, Software, Transcription |
| Package Short Url | https://bioconductor.org/packages/NetActivity/ |
Citation
From within R, enter citation("NetActivity"):
Carlos Ruiz-Arenas. NetActivity: Compute gene set scores from a deep learning framework. doi:10.18129/B9.bioc.NetActivity, R package version 1.14.0, https://bioconductor.org/packages/NetActivity.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | NetActivity_1.14.0.tar.gz |
| Windows binary (x86_64) | NetActivity_1.14.0.zip |
| macOS binary (arm64) | NetActivity_1.14.0.tgz |
| macOS binary (x86_64) | NetActivity_1.14.0.tgz |
Dependencies
Depends: R (>= 4.1.0)
Imports: airway, DelayedArray, DelayedMatrixStats, DESeq2, methods, methods, NetActivityData, SummarizedExperiment, utils
Suggests: AnnotationDbi, BiocStyle, Fletcher2013a, knitr, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0), tidyverse