Package: funOmics 1.7.0
Elisa Gomez de Lope
funOmics: Aggregating Omics Data into Higher-Level Functional Representations
The 'funOmics' package ggregates or summarizes omics data into higher level functional representations such as GO terms gene sets or KEGG metabolic pathways. The aggregated data matrix represents functional activity scores that facilitate the analysis of functional molecular sets while allowing to reduce dimensionality and provide easier and faster biological interpretations. Coordinated functional activity scores can be as informative as single molecules!
Authors:
funOmics_1.7.0.tar.gz
funOmics_1.7.0.zip(r-4.7)funOmics_1.7.0.zip(r-4.6)funOmics_1.7.0.zip(r-4.5)
funOmics_1.7.0.tgz(r-4.6-any)funOmics_1.7.0.tgz(r-4.5-any)
funOmics_1.7.0.tar.gz(r-4.7-any)funOmics_1.7.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
card.svg |card.png
funOmics/json (API)
NEWS
| # Install 'funOmics' in R: |
| install.packages('funOmics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/elisagdelope/funomics/issues
On BioConductor:funOmics-1.7.0(bioc 3.24)funOmics-1.6.0(bioc 3.23)
softwaretranscriptomicsmetabolomicsproteomicspathwaysgokegg
Last updated from:5a5f758fa8. Checks:8 NOTE, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 186 | ||
| linux-devel-x86_64 | NOTE | 301 | ||
| source / vignettes | OK | 500 | ||
| linux-release-x86_64 | NOTE | 382 | ||
| macos-release-arm64 | NOTE | 299 | ||
| macos-oldrel-arm64 | NOTE | 216 | ||
| windows-devel | NOTE | 239 | ||
| windows-release | NOTE | 315 | ||
| windows-oldrel | NOTE | 304 | ||
| wasm-release | FAIL | 171 |
Exports:get_kegg_setsshort_sets_detailsummarize_pathway_level
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiocManagerBiostringsbitbit64blobcachemcliclustercodetoolscolorspacecpp11crayoncurlDBIdigestdoParalleldplyrfarverfastmapforeachgenericsggplot2gluegridBasegtablehttrIRangesisobanditeratorsjsonliteKEGGRESTlabelinglifecyclemagrittrmemoisemimeNMFopensslorg.Hs.eg.dbpathifierpillarpkgconfigplyrpngprincurveR.methodsS3R.ooR6RColorBrewerRcppregistryreshape2rlangrngtoolsRSQLiteS4VectorsS7scalesSeqinfostringistringrsystibbletidyselectutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregating Omics Data into Higher-Level Functional Representations | funOmics-package funOmics |
| Retrieves KEGG pathway gene sets for a specified organism and gene ID type. | get_kegg_sets |
| Retrieve details and information about short molecular sets | short_sets_detail |
| Aggregates or summarizes omics data into higher-level functional representations that can be interpreted as functional activity scores or measures. | summarize_pathway_level |
