famat: Functional analysis of metabolic and transcriptomic data

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.

Getting started

Package details

AuthorEmilie Secherre [aut, cre] (<https://orcid.org/0000-0001-5343-6324>)
Bioconductor views FunctionalPrediction GO GeneSetEnrichment KEGG Pathways Reactome
MaintainerEmilie Secherre <emisecherre@gmail.com>
URL https://github.com/emiliesecherre/famat
Package repositoryView on Bioconductor
Installation Install the latest version of this package by entering the following in R:
if (!requireNamespace("BiocManager", quietly = TRUE))


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famat documentation built on Nov. 8, 2020, 5:56 p.m.