Functional analysis of metabolic and transcriptomic data

Bioconductor version: Release (3.19)

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 (from within R, enter citation("famat")):


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Reference Manual PDF


biocViews FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Pathways, Reactome, Software
Version 1.14.0
In Bioconductor since BioC 3.12 (R-4.0) (3.5 years)
License GPL-3
Depends R (>= 4.0)
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
System Requirements
URL https://github.com/emiliesecherre/famat
Bug Reports https://github.com/emiliesecherre/famat/issues
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Suggests BiocStyle, knitr, rmarkdown, testthat, BiocManager
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Source Package famat_1.14.0.tar.gz
Windows Binary famat_1.14.0.zip (64-bit only)
macOS Binary (x86_64) famat_1.14.0.tgz
macOS Binary (arm64) famat_1.14.0.tgz
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Bioc Package Browser https://code.bioconductor.org/browse/famat/
Package Short Url https://bioconductor.org/packages/famat/
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