famat

This is the development version of famat; for the stable release version, see famat.

Functional analysis of metabolic and transcriptomic data

Bioconductor version: Development (3.18)

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")):

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	PDF
NEWS	Text

Details

biocViews	FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Pathways, Reactome, Software
Version	1.11.0
In Bioconductor since	BioC 3.12 (R-4.0) (3 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
Linking To
Suggests	BiocStyle, knitr, rmarkdown, testthat, BiocManager
System Requirements
Enhances
URL	https://github.com/emiliesecherre/famat
Bug Reports	https://github.com/emiliesecherre/famat/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	famat_1.11.0.tar.gz
Windows Binary	famat_1.11.0.zip
macOS Binary (x86_64)	famat_1.11.0.tgz
macOS Binary (arm64)	famat_1.11.0.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