famat
This is the released version of famat; for the devel version, see famat.
Functional analysis of metabolic and transcriptomic data
Bioconductor version: Release (3.23)
Famat is made to collect data about lists of genes and metabolites provided by user, and to visualize it through a Shiny app. Information collected is: - Pathways containing some of the user's genes and metabolites (obtained using a pathway enrichment analysis). - Direct interactions between user's elements inside pathways. - Information about elements (their identifiers and descriptions). - Go terms enrichment analysis performed on user's genes. The Shiny app is composed of: - information about genes, metabolites, and direct interactions between them inside pathways. - an heatmap showing which elements from the list are in pathways (pathways are structured in hierarchies). - hierarchies of enriched go terms using Molecular Function and Biological Process.
Author: Mathieu Charles [aut, cre]
Maintainer: Mathieu Charles <mathieu.charles at inrae.fr>
citation("famat")):
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("famat")
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("famat")| famat | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Pathways, Reactome, Software |
| Version | 1.22.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (6 years) |
| License | GPL-3 |
| Depends | R (>= 4.3) |
| Imports | KEGGREST, mgcv, stats, BiasedUrn, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db, ReactomePA, enrichplot |
| System Requirements | |
| URL | https://github.com/emiliesecherre/famat |
| Bug Reports | https://github.com/emiliesecherre/famat/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, BiocManager |
| 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 | famat_1.22.0.tar.gz |
| Windows Binary (x86_64) | famat_1.22.0.zip |
| macOS Binary (big-sur-x86_64) | famat_1.22.0.tgz |
| macOS Binary (sonoma-arm64) | famat_1.22.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/famat |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/famat |
| Bioc Package Browser | https://code.bioconductor.org/browse/famat/ |
| Package Short Url | https://bioconductor.org/packages/famat/ |
| Package Downloads Report | Download Stats |