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funOmics

Aggregating Omics Data into Higher-Level Functional Representations

Bioconductor version: 3.23 · Package version: 1.6.0

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!

Installation

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

BiocManager::install("funOmics")

Details

MaintainerElisa Gomez de Lope <elisa.gomezdelope@uni.lu>
AuthorElisa Gomez de Lope [aut, cre] (ORCID: <https://orcid.org/0000-0002-7115-7393>), Enrico Glaab [ctb] (ORCID: <https://orcid.org/0000-0003-3977-7469>)
LicenseMIT + file LICENSE
URLhttps://github.com/elisagdelope/funomics
Bug Reportshttps://github.com/elisagdelope/funomics/issues
Downloads rank137
Source branchRELEASE_3_23
biocViewsGO, KEGG, Metabolomics, Pathways, Proteomics, Software, Transcriptomics

Documentation

Download

Dependencies

Depends: R (>= 4.4.0), NMF

Imports: NMF, pathifier, stats, KEGGREST, AnnotationDbi, org.Hs.eg.db, dplyr, stringr

Suggests: knitr, rmarkdown, testthat (>= 3.0.0), MultiAssayExperiment, SummarizedExperiment, airway