FELLA
This is the released version of FELLA; for the devel version, see FELLA.
Interpretation and enrichment for metabolomics data
Bioconductor version: Release (3.23)
Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.
Author: Sergio Picart-Armada [aut, cre], Francesc Fernandez-Albert [aut], Alexandre Perera-Lluna [aut]
Maintainer: Sergio Picart-Armada <sergi.picart at upc.edu>
citation("FELLA")):
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("FELLA")
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("FELLA")| Example: a fatty liver study on Mus musculus | R Script | |
| Example: oxybenzone exposition in gilt-head bream | R Script | |
| FELLA | R Script | |
| Quick start | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GO, GraphAndNetwork, KEGG, Metabolomics, Network, NetworkEnrichment, Pathways, Software |
| Version | 1.32.0 |
| In Bioconductor since | BioC 3.7 (R-3.5) (8.5 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0) |
| Imports | methods, igraph, Matrix, KEGGREST, plyr, stats, graphics, utils |
| System Requirements | |
| URL |
See More
| Suggests | shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim |
| 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 | FELLA_1.32.0.tar.gz |
| Windows Binary (x86_64) | FELLA_1.32.0.zip |
| macOS Binary (big-sur-x86_64) | FELLA_1.32.0.tgz |
| macOS Binary (sonoma-arm64) | FELLA_1.32.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/FELLA |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/FELLA |
| Bioc Package Browser | https://code.bioconductor.org/browse/FELLA/ |
| Package Short Url | https://bioconductor.org/packages/FELLA/ |
| Package Downloads Report | Download Stats |