This is the released version of famat; for the devel version, see famat.
Functional analysis of metabolic and transcriptomic dataBioconductor version: Release (3.21)
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] ORCID: 0000-0001-5343-6324
Maintainer: Mathieu Charles <mathieu.charles at inrae.fr>
Citation (from within R, entercitation("famat")): Installation
To install this package, start R (version "4.5") 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.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("famat")Follow Installation instructions to use this package in your R session.
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