Package: famat 1.23.0

Mathieu Charles

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.

Authors:Mathieu Charles [aut, cre]

famat_1.23.0.tar.gz
famat_1.23.0.zip(r-4.7)famat_1.23.0.zip(r-4.6)famat_1.23.0.zip(r-4.5)
famat_1.23.0.tgz(r-4.6-any)famat_1.23.0.tgz(r-4.5-any)
famat_1.23.0.tar.gz(r-4.7-any)famat_1.23.0.tar.gz(r-4.6-any)
famat_1.23.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
famat/json (API)
NEWS

# Install 'famat' in R:
install.packages('famat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/emiliesecherre/famat/issues

Datasets:
  • compl_data_result - Output of 'compl_data' function
  • genes - List of genes.
  • interactions_result - Output of 'interactions' function
  • listk - Pathway enrichment analysis results for KEGG pathways.
  • listr - Pathway enrichment analysis results for Reactome pathways.
  • listw - Pathway enrichment analysis results for Wikipathways pathways.
  • meta - List of metabolites.
  • MPINetData - The variables in the environment variable 'MPINetData' of the system

On BioConductor:famat-1.23.0(bioc 3.24)famat-1.22.0(bioc 3.23)

functionalpredictiongenesetenrichmentpathwaysgoreactomekeggcompoundgene-ontologygenesshiny

4.26 score 1 stars 5 scripts 329 downloads 4 exports 164 dependencies

Last updated from:58f2c76c9e. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE268
linux-devel-x86_64WARNING739
source / vignettesOK484
linux-release-x86_64WARNING706
macos-release-arm64WARNING494
macos-oldrel-arm64WARNING406
windows-develWARNING579
windows-releaseWARNING610
windows-oldrelWARNING561
wasm-releaseOK258

Exports:compl_datainteractionspath_enrichrshiny

Dependencies:aisdkAnnotationDbiapeaplotaskpassbase64encBiasedUrnBiobaseBiocGenericsBiostringsbitbit64bitopsblobbslibcachemcallrclicliprclusterclusterProfilercommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdir.expiryDOSEdplyrDTenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggtangleggtreeglueGO.dbGOSemSimgprofiler2graphgraphitegraphlayoutsgridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimenlmeontologyIndexopensslorg.Hs.eg.dbotelpatchworkpillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRCurlreactome.dbReactomePAreadrreshape2rjsonrlangrmarkdownRSQLiterWikiPathwaysS4VectorsS7sassscalesscatterpieSeqinfoshinyshinyBSshinydashboardsourcetoolsstringistringrsyssystemfontstibbletidydrtidygraphtidyrtidyselecttidytreetimechangetinytextreeiotweenrtzdbutf8vctrsviridisviridisLitevroomwithrxfunXMLxtableXVectoryamlyulab.utils

famat

Emilie Secherre

Rendered fromfamat.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2026-01-26
Started: 2020-09-29