famat
This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see famat.
Functional analysis of metabolic and transcriptomic data
Bioconductor version: 3.12
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("famat")):
Installation
To install this package, start R (version "4.0") 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.
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 | ||
| NEWS | Text |
Details
| biocViews | FunctionalPrediction, GO, GeneSetEnrichment, KEGG, Pathways, Reactome, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.12 (R-4.0) (3.5 years) |
| 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 |
| System Requirements | |
| URL | https://github.com/emiliesecherre/famat |
| Bug Reports | https://github.com/emiliesecherre/famat/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat, BiocManager |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | famat_1.0.0.tar.gz |
| Windows Binary | famat_1.0.0.zip |
| macOS 10.13 (High Sierra) | famat_1.0.0.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 |
| Old Source Packages for BioC 3.12 | Source Archive |