NetActivity
This is the released version of NetActivity; for the devel version, see NetActivity.
Compute gene set scores from a deep learning framework
Bioconductor version: Release (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("NetActivity")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.14.0 |
| In Bioconductor since | BioC 3.16 (R-4.2) (4 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_1.14.0.tar.gz |
| Windows Binary (x86_64) | NetActivity_1.14.0.zip |
| macOS Binary (big-sur-x86_64) | NetActivity_1.14.0.tgz |
| macOS Binary (sonoma-arm64) | NetActivity_1.14.0.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 |