funOmics
This is the development version of funOmics; for the stable release version, see funOmics.
Aggregating Omics Data into Higher-Level Functional Representations
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Elisa Gomez de Lope <elisa.gomezdelope at uni.lu>
citation("funOmics")):
Installation
To install this package, start R (version "4.5") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | GO, KEGG, Metabolomics, Pathways, Proteomics, Software, Transcriptomics |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| 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 |
| 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 | funOmics_1.1.0.tar.gz |
| Windows Binary (x86_64) | funOmics_1.1.0.zip (64-bit only) |
| macOS Binary (x86_64) | funOmics_1.1.0.tgz |
| macOS Binary (arm64) | funOmics_1.1.0.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 |