Package: netOmics 1.11.0
Antoine Bodein
netOmics: Multi-Omics (time-course) network-based integration and interpretation
netOmics is a multi-omics networks builder and explorer. It uses a combination of network inference algorithms and and knowledge-based graphs to build multi-layered networks. The package can be combined with timeOmics to incorporate time-course expression data and build sub-networks from multi-omics kinetic clusters. Finally, from the generated multi-omics networks, propagation analyses allow the identification of missing biological functions (1), multi-omics mechanisms (2) and molecules between kinetic clusters (3). This helps to resolve complex regulatory mechanisms.
Authors:
netOmics_1.11.0.tar.gz
netOmics_1.11.0.zip(r-4.5)netOmics_1.11.0.zip(r-4.4)netOmics_1.11.0.zip(r-4.3)
netOmics_1.11.0.tgz(r-4.4-any)netOmics_1.11.0.tgz(r-4.3-any)
netOmics_1.11.0.tar.gz(r-4.5-noble)netOmics_1.11.0.tar.gz(r-4.4-noble)
netOmics_1.11.0.tgz(r-4.4-emscripten)netOmics_1.11.0.tgz(r-4.3-emscripten)
netOmics.pdf |netOmics.html✨
netOmics/json (API)
| # Install 'netOmics' in R: |
| install.packages('netOmics', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/abodein/netomics/issues
- hmp_T2D - Hmp_T2D
On BioConductor:netOmics-1.11.0(bioc 3.20)netOmics-1.10.0(bioc 3.19)
Last updated 2 months agofrom:bedd645b29
Exports:combine_layersget_graph_statsget_grnget_interaction_from_correlationget_interaction_from_databaseget_interaction_from_ORAplot_rwr_subnetworkrandom_walk_restartrwr_find_closest_typerwr_find_seeds_between_attributessummary_plot_rwr_attributes
Dependencies:AnnotationDbiaskpassbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobbslibcachemclicolorspacecpp11crayoncrosstalkcurldata.tableDBIdigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsGenomeInfoDbGenomeInfoDbDataggplot2glueGO.dbgprofiler2gridExtragtablehighrhtmltoolshtmlwidgetshttrigraphinfotheoIRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglaterlatticelazyevallifecyclemagrittrMASSMatrixmemoisemgcvmimeminetmunsellnlmeopensslpillarpkgconfigplogrplotlypngpromisespurrrR6rappdirsRColorBrewerRcppRCurlrlangrmarkdownRSQLiteS4VectorssassscalesstringistringrsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXVectoryamlzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Combine layers | combine_layers |
| Get GO info | get_go_info |
| Get graph statistics | get_graph_stats |
| Gene Regulatory Network | get_grn |
| Interaction_from_correlation | get_interaction_from_correlation |
| Get interaction from database | get_interaction_from_database |
| Get interaction from ORA enrichment analysis | get_interaction_from_ORA |
| ORA enrichment analysis | get_ORA |
| hmp_T2D | hmp_T2D |
| netOmics: network-based multi-omics integration and interpretation | netOmics-package netOmics |
| Plot RWR subnetwork | plot_rwr_subnetwork |
| Random Walk with Restart | random_walk_restart |
| RWR Find closest nodes | rwr_find_closest_type |
| RWR Find seeds between attributes | rwr_find_seeds_between_attributes |
| Summary Plot RWR attributes | summary_plot_rwr_attributes |
