funOmics

This is the development version of funOmics; to use it, please install the devel version of Bioconductor.

Aggregating Omics Data into Higher-Level Functional Representations


Bioconductor version: Development (3.20)

The 'funOmics' package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!

Author: Elisa Gomez de Lope [aut, cre] , Enrico Glaab [ctb]

Maintainer: Elisa Gomez de Lope <elisa.gomezdelope at uni.lu>

Citation (from within R, enter citation("funOmics")):

Installation

To install this package, start R (version "4.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("funOmics")

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("funOmics")
funOmics HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews GO, KEGG, Metabolomics, Pathways, Proteomics, Software, Transcriptomics
Version 0.99.8
In Bioconductor since BioC 3.20 (R-4.4)
License MIT + file LICENSE
Depends R (>= 4.4.0), NMF
Imports NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db, dplyr, stringr
System Requirements
URL https://github.com/elisagdelope/funomics
Bug Reports https://github.com/elisagdelope/funomics/issues
See More
Suggests knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment, SummarizedExperiment, airway
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Package Archives

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

Source Package funOmics_0.99.8.tar.gz
Windows Binary funOmics_0.99.8.zip
macOS Binary (x86_64) funOmics_0.99.8.tgz
macOS Binary (arm64) funOmics_0.99.8.tgz
Source Repository git clone https://git.bioconductor.org/packages/funOmics
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/funOmics
Bioc Package Browser https://code.bioconductor.org/browse/funOmics/
Package Short Url https://bioconductor.org/packages/funOmics/
Package Downloads Report Download Stats