famat

DOI: 10.18129/B9.bioc.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 (3.13)

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: Emilie Secherre [aut, cre]

Maintainer: Emilie Secherre <emisecherre at gmail.com>

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

Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("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")

 

HTML R Script famat
PDF   Reference Manual
Text   NEWS

Details

biocViews FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Pathways, Reactome, Software
Version 1.1.1
In Bioconductor since BioC 3.12 (R-4.0) (< 6 months)
License GPL-3
Depends R (>= 4.0)
Imports KEGGREST, MPINet, dplyr, gprofiler2, rWikiPathways, reactome.db, stringr, GO.db, ontologyIndex, tidyr, shiny, shinydashboard, shinyBS, plotly, magrittr, DT, clusterProfiler, org.Hs.eg.db
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, testthat, BiocManager
SystemRequirements
Enhances
URL https://github.com/emiliesecherre/famat
BugReports 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_1.1.1.tar.gz
Windows Binary famat_1.1.1.zip
macOS 10.13 (High Sierra) famat_1.1.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/famat
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/famat
Package Short Url https://bioconductor.org/packages/famat/
Package Downloads Report Download Stats

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