Package: famat 1.17.0
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_1.17.0.tar.gz
famat_1.17.0.zip(r-4.5)famat_1.17.0.zip(r-4.4)famat_1.17.0.zip(r-4.3)
famat_1.17.0.tgz(r-4.4-any)famat_1.17.0.tgz(r-4.3-any)
famat_1.17.0.tar.gz(r-4.5-noble)famat_1.17.0.tar.gz(r-4.4-noble)
famat_1.17.0.tgz(r-4.4-emscripten)famat_1.17.0.tgz(r-4.3-emscripten)
famat.pdf |famat.html✨
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
- MPINetData - The variables in the environment variable 'MPINetData' of the system
- 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.
On BioConductor:famat-1.17.0(bioc 3.21)famat-1.16.0(bioc 3.20)
functionalpredictiongenesetenrichmentpathwaysgoreactomekeggcompoundgene-ontologygenesshiny
Last updated 2 months agofrom:3a4f53d659. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 19 2024 |
| R-4.5-win | NOTE | Dec 19 2024 |
| R-4.5-linux | NOTE | Dec 19 2024 |
| R-4.4-win | NOTE | Dec 19 2024 |
| R-4.4-mac | ERROR | Dec 19 2024 |
| R-4.3-win | NOTE | Dec 19 2024 |
| R-4.3-mac | ERROR | Dec 19 2024 |
Exports:compl_datainteractionspath_enrichrshiny
Dependencies:AnnotationDbiapeaplotaskpassbase64encBHBiasedUrnBiobaseBiocGenericsBiocParallelBiostringsbitbit64bitopsblobbslibcachemclicliprclusterProfilercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdigestDOSEdplyrDTenrichplotevaluatefansifarverfastmapfastmatchfgseafontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggforceggfunggnewscaleggplot2ggplotifyggrepelggtangleggtreeglueGO.dbGOSemSimgprofiler2gridExtragridGraphicsgsongtablehighrhmshtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclelubridatemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeontologyIndexopensslorg.Hs.eg.dbpatchworkpillarpkgconfigplogrplotlyplyrpngpolyclipprettyunitsprogresspromisespurrrqvalueR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppEigenRCurlreactome.dbreadrreshape2rjsonrlangrmarkdownRSQLiterWikiPathwaysS4VectorssassscalesscatterpieshinyshinyBSshinydashboardsnowsourcetoolsstringistringrsyssystemfontstibbletidyrtidyselecttidytreetimechangetinytextreeiotweenrtzdbUCSC.utilsutf8vctrsviridisLitevroomwithrxfunXMLxtableXVectoryamlyulab.utilszlibbioc
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 |
