Introduction | Installation | path_enrich | interactions | compl_data | rshiny | Conclusion: how to use famat | References | Session Info
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:
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✨
DESCRIPTION |NEWS
card.svg |card.png
famat/json (API)
| # 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
Last updated from:58f2c76c9e. Checks:1 NOTE, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 310 | ||
| linux-devel-x86_64 | WARNING | 635 | ||
| source / vignettes | OK | 470 | ||
| linux-release-x86_64 | WARNING | 662 | ||
| macos-release-arm64 | WARNING | 464 | ||
| macos-oldrel-arm64 | WARNING | 377 | ||
| windows-devel | WARNING | 615 | ||
| windows-release | WARNING | 534 | ||
| windows-oldrel | WARNING | 530 | ||
| wasm-release | OK | 286 |
Exports:compl_datainteractionspath_enrichrshiny
Dependencies:aisdkAnnotationDbiapeaplotaskpassbase64encBiasedUrnBiobaseBiocGenericsBiostringsbitbit64bitopsblobbslibcachemcallrclicliprclusterclusterProfilercommonmarkcpp11crayoncrosstalkcurldata.tableDBIdigestdir.expiryDOSEdplyrDTenrichitenrichplotevaluatefarverfastmapfilelockfontawesomefontBitstreamVerafontLiberationfontquiverfsgdtoolsgenericsggforceggfunggiraphggnewscaleggplot2ggplotifyggraphggrepelggtangleggtreeglueGO.dbGOSemSimgprofiler2graphgraphitegraphlayoutsgridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimenlmeontologyIndexopensslorg.Hs.eg.dbotelpatchworkpillarpkgconfigplotlyplyrpngpolyclipprettyunitsprocessxprogresspromisespspurrrqvalueR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRCurlreactome.dbReactomePAreadrreshape2rjsonrlangrmarkdownRSQLiterWikiPathwaysS4VectorsS7sassscalesscatterpieSeqinfoshinyshinyBSshinydashboardsourcetoolsstringistringrsyssystemfontstibbletidydrtidygraphtidyrtidyselecttidytreetimechangetinytextreeiotweenrtzdbutf8vctrsviridisviridisLitevroomwithrxfunXMLxtableXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Data preparation for Shiny interface | compl_data |
| Output of 'compl_data' function | compl_data_result |
| List of genes. | genes |
| Interactions between genes and metabolites | interactions |
| Output of 'interactions' function | interactions_result |
| Pathway enrichment analysis results for KEGG pathways. | listk |
| Pathway enrichment analysis results for Reactome pathways. | listr |
| Pathway enrichment analysis results for Wikipathways pathways. | listw |
| List of metabolites. | meta |
| The variables in the environment variable 'MPINetData' of the system | consensusPath getBackground getnodeseq getpathList('KEGG') getStr MPINetData |
| Pathway enrichment analysis | path_enrich |
| Shiny interface | rshiny |
