Package: OmnipathR 3.13.1
OmnipathR: OmniPath web service client and more
A client for the OmniPath web service (https://www.omnipathdb.org) and many other resources. It also includes functions to transform and pretty print some of the downloaded data, functions to access a number of other resources such as BioPlex, ConsensusPathDB, EVEX, Gene Ontology, Guide to Pharmacology (IUPHAR/BPS), Harmonizome, HTRIdb, Human Phenotype Ontology, InWeb InBioMap, KEGG Pathway, Pathway Commons, Ramilowski et al. 2015, RegNetwork, ReMap, TF census, TRRUST and Vinayagam et al. 2011. Furthermore, OmnipathR features a close integration with the NicheNet method for ligand activity prediction from transcriptomics data, and its R implementation `nichenetr` (available only on github).
Authors:
OmnipathR_3.13.1.tar.gz
OmnipathR_3.13.1.zip(r-4.5)OmnipathR_3.13.1.zip(r-4.4)OmnipathR_3.13.1.zip(r-4.3)
OmnipathR_3.13.1.tgz(r-4.4-any)OmnipathR_3.13.1.tgz(r-4.3-any)
OmnipathR_3.13.1.tar.gz(r-4.5-noble)OmnipathR_3.13.1.tar.gz(r-4.4-noble)
OmnipathR_3.13.1.tgz(r-4.4-emscripten)OmnipathR_3.13.1.tgz(r-4.3-emscripten)
OmnipathR.pdf |OmnipathR.html✨
OmnipathR/json (API)
NEWS
# Install 'OmnipathR' in R: |
install.packages('OmnipathR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/saezlab/omnipathr/issues
On BioConductor:OmnipathR-3.13.1(bioc 3.20)OmnipathR-3.11.10(bioc 3.19)
Last updated 1 months agofrom:1cdbb59c0e
Exports:all_uniprot_acsall_uniprotsancestorsannotated_networkannotation_categoriesbiomart_querybioplex_allbioplex_hct116_1bioplex1bioplex2bioplex3bma_motif_esbma_motif_vscollectricommon_nameconsensuspathdb_downloadconsensuspathdb_raw_tablecookiecurated_ligand_receptor_interactionscurated_ligrec_statsdatabase_summarydatasets_one_columndescendantsdorotheaensembl_datasetensembl_id_mapping_tableensembl_id_typeensembl_nameensembl_organismsensembl_organisms_rawensembl_orthologyensure_igraphenzsub_graphevex_downloadevidencesextra_attr_valuesextra_attrsextra_attrs_to_colsfilter_by_resourcefilter_evidencesfilter_extra_attrsfilter_intercellfilter_intercell_networkfind_all_pathsfrom_evidencesget_annotation_databasesget_annotation_resourcesget_complex_genesget_complex_resourcesget_complexes_databasesget_dbget_enzsub_resourcesget_interaction_databasesget_interaction_resourcesget_intercell_categoriesget_intercell_classesget_intercell_generic_categoriesget_intercell_resourcesget_ontology_dbget_ptms_databasesget_resourcesget_signed_ptmsgiant_componentgo_annot_downloadgo_annot_slimgo_ontology_downloadgraph_interactionguide2pharma_downloadharmonizome_downloadhas_extra_attrshomologene_downloadhomologene_organismshomologene_rawhomologene_uniprot_orthologyhpo_downloadhtridb_downloadimport_all_interactionsimport_AllInteractionsimport_dorothea_interactionsimport_intercell_networkimport_kinaseextra_interactionsimport_KinaseExtra_Interactionsimport_ligrecextra_interactionsimport_LigrecExtra_Interactionsimport_lncrna_mrna_interactionsimport_mirnatarget_interactionsimport_miRNAtarget_Interactionsimport_omnipath_annotationsimport_Omnipath_annotationsimport_OmniPath_annotationsimport_omnipath_complexesimport_Omnipath_complexesimport_OmniPath_complexesimport_omnipath_enzsubimport_omnipath_interactionsimport_Omnipath_Interactionsimport_OmniPath_Interactionsimport_omnipath_intercellimport_Omnipath_intercellimport_OmniPath_intercellimport_Omnipath_PTMSimport_OmniPath_PTMSimport_pathwayextra_interactionsimport_PathwayExtra_Interactionsimport_post_translational_interactionsimport_small_molecule_protein_interactionsimport_tf_mirna_interactionsimport_tf_target_interactionsimport_tfregulons_interactionsimport_transcriptional_interactionsinbiomap_downloadinbiomap_rawinteraction_datasetsinteraction_graphinteraction_typesintercell_categoriesintercell_consensus_filteris_ontology_idis_swissprotis_tremblis_uniprotkegg_infokegg_openkegg_pathway_annotationskegg_pathway_downloadkegg_pathway_listkegg_pathways_downloadkegg_picturekegg_processlatin_nameload_dbncbi_taxidnichenet_build_modelnichenet_expression_datanichenet_gr_networknichenet_gr_network_evexnichenet_gr_network_harmonizomenichenet_gr_network_htridbnichenet_gr_network_omnipathnichenet_gr_network_pathwaycommonsnichenet_gr_network_regnetworknichenet_gr_network_remapnichenet_gr_network_trrustnichenet_ligand_activitiesnichenet_ligand_target_linksnichenet_ligand_target_matrixnichenet_lr_networknichenet_lr_network_guide2pharmanichenet_lr_network_omnipathnichenet_lr_network_ramilowskinichenet_mainnichenet_networksnichenet_optimizationnichenet_remove_orphan_ligandsnichenet_results_dirnichenet_signaling_networknichenet_signaling_network_cpdbnichenet_signaling_network_evexnichenet_signaling_network_harmonizomenichenet_signaling_network_inbiomapnichenet_signaling_network_omnipathnichenet_signaling_network_pathwaycommonsnichenet_signaling_network_vinayagamnichenet_testnichenet_workaroundsobo_parseroma_codeoma_organismsoma_pairwiseoma_pairwise_genesymbolsoma_pairwise_translatedomnipathomnipath_cache_autocleanomnipath_cache_cleanomnipath_cache_clean_dbomnipath_cache_download_readyomnipath_cache_filter_versionsomnipath_cache_getomnipath_cache_keyomnipath_cache_latest_or_newomnipath_cache_latest_versionomnipath_cache_loadomnipath_cache_move_inomnipath_cache_removeomnipath_cache_saveomnipath_cache_searchomnipath_cache_set_extomnipath_cache_update_statusomnipath_cache_wipeomnipath_get_config_pathomnipath_load_configomnipath_logomnipath_logfileomnipath_msgomnipath_reset_configomnipath_save_configomnipath_set_cachediromnipath_set_console_loglevelomnipath_set_logfile_loglevelomnipath_set_loglevelomnipath_show_dbomnipath_unlock_cache_dbonly_fromontology_ensure_idontology_ensure_nameontology_name_idorganism_fororthology_translate_columnpathwaycommons_downloadpivot_annotationspreppi_downloadpreppi_filterprint_bma_motif_esprint_bma_motif_vsprint_interactionsprint_path_esprint_path_vsprintPath_esprintPath_vsptms_graphpubmed_openquery_inforamilowski_downloadregnetwork_directionsregnetwork_downloadrelations_list_to_tablerelations_table_to_graphrelations_table_to_listremap_dorothea_downloadremap_filteredremap_tf_target_downloadresource_inforesources_colnameresources_inshow_networksimplify_intercell_networkstatic_tablestatic_tablessubnetworkswap_relationsswissprots_onlytfcensus_downloadtranslate_idstrembls_onlytrrust_downloaduniprot_full_id_mapping_tableuniprot_genesymbol_cleanupuniprot_id_mapping_tableuniprot_id_typeuniprot_idmapping_id_typesunique_intercell_networkunnest_evidencesuploadlists_id_typevinayagam_downloadwalk_ontology_treewith_extra_attrswith_referenceszenodo_download
Dependencies:askpassbackportsbase64encbitbit64bslibcachemcellrangercheckmateclicliprcpp11crayoncurldigestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhmshtmltoolshttrigraphjquerylibjsonliteknitrlaterlatticelifecycleloggerlubridatemagrittrMatrixmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR6rappdirsRcppreadrreadxlrematchrlangrmarkdownrvestsassselectrstringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsvroomwithrxfunxml2yaml
Building protein networks around drug-targets using OmnipathR
Rendered fromdrug_targets.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2024-03-21
Started: 2020-03-28
The database manager in OmnipathR
Rendered fromdb_manager.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2022-10-10
Started: 2022-02-20
Resource specific interaction attributes
Rendered fromextra_attrs.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2022-02-15
Started: 2022-02-15
OmniPath Bioconductor workshop
Rendered frombioc_workshop.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2022-01-15
Started: 2021-03-16
OmnipathR: an R client for the OmniPath web service
Rendered fromomnipath_intro.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2024-03-21
Started: 2020-10-02
Pathway construction
Rendered frompaths.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2023-04-09
Started: 2021-08-04
Using NicheNet with OmnipathR
Rendered fromnichenet.Rmd
usingknitr::rmarkdown
on Jul 02 2024.Last update: 2021-07-24
Started: 2021-03-12