Package: OmnipathR 3.15.0

Denes Turei

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:Alberto Valdeolivas [aut], Denes Turei [cre, aut], Attila Gabor [aut], Diego Mananes [aut], Aurelien Dugourd [aut]

OmnipathR_3.15.0.tar.gz
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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'))

Peer review:

Bug tracker:https://github.com/saezlab/omnipathr/issues

Pkgdown:https://saezlab.github.io

On BioConductor:OmnipathR-3.15.0(bioc 3.21)OmnipathR-3.14.0(bioc 3.20)

graphandnetworknetworkpathwayssoftwarethirdpartyclientdataimportdatarepresentationgenesignalinggeneregulationsystemsbiologytranscriptomicssinglecellannotationkeggcomplexesenzyme-ptmnetworksnetworks-biologyomnipathproteins

11.73 score 118 stars 2 packages 236 scripts 1.1k downloads 3 mentions 294 exports 82 dependencies

Last updated 2 months agofrom:bc4d2dd956. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 18 2024
R-4.5-winERRORDec 18 2024
R-4.5-linuxERRORDec 18 2024
R-4.4-winERRORDec 18 2024
R-4.4-macERRORDec 18 2024
R-4.3-winERRORDec 18 2024
R-4.3-macERRORDec 18 2024

Exports:all_interactionsall_uniprot_acsall_uniprotsancestorsannotated_networkannotation_categoriesannotation_resourcesannotationsbiomart_querybioplex_allbioplex_hct116_1bioplex1bioplex2bioplex3bma_motif_esbma_motif_vschalmers_gemchalmers_gem_id_mapping_tablechalmers_gem_id_typechalmers_gem_metaboliteschalmers_gem_networkchalmers_gem_rawchalmers_gem_reactionscollectricommon_namecomplex_genescomplex_resourcescomplexesconfig_pathconsensuspathdb_downloadconsensuspathdb_raw_tablecookiecosmos_pkncurated_ligand_receptor_interactionscurated_ligrec_statsdatabase_summarydatasets_one_columndescendantsdorotheaensembl_datasetensembl_id_mapping_tableensembl_id_typeensembl_nameensembl_organismsensembl_organisms_rawensembl_orthologyensure_igraphenzsub_graphenzsub_resourcesenzyme_substrateevex_downloadevidencesextra_attr_valuesextra_attrsextra_attrs_to_colsfilter_by_resourcefilter_evidencesfilter_extra_attrsfilter_intercellfilter_intercell_networkfind_all_pathsfrom_evidencesget_annotation_resourcesget_complex_genesget_complex_resourcesget_dbget_enzsub_resourcesget_interaction_resourcesget_intercell_categoriesget_intercell_generic_categoriesget_intercell_resourcesget_ontology_dbget_resourcesgiant_componentgo_annot_downloadgo_annot_slimgo_ontology_downloadgraph_interactionguide2pharma_downloadharmonizome_downloadhas_extra_attrshmdb_id_mapping_tablehmdb_id_typehmdb_metabolite_fieldshmdb_protein_fieldshmdb_tablehomologene_downloadhomologene_organismshomologene_rawhomologene_uniprot_orthologyhpo_downloadhtridb_downloadid_translation_resourcesid_typesimport_all_interactionsimport_dorothea_interactionsimport_intercell_networkimport_kinaseextra_interactionsimport_ligrecextra_interactionsimport_lncrna_mrna_interactionsimport_mirnatarget_interactionsimport_omnipath_annotationsimport_omnipath_complexesimport_omnipath_enzsubimport_omnipath_interactionsimport_omnipath_intercellimport_pathwayextra_interactionsimport_post_translational_interactionsimport_small_molecule_protein_interactionsimport_tf_mirna_interactionsimport_tf_target_interactionsimport_transcriptional_interactionsinbiomap_downloadinbiomap_rawinteraction_datasetsinteraction_graphinteraction_resourcesinteraction_typesintercellintercell_categoriesintercell_consensus_filterintercell_generic_categoriesintercell_networkintercell_resourcesintercell_summaryis_ontology_idis_swissprotis_tremblis_uniprotkegg_infokegg_openkegg_pathway_annotationskegg_pathway_downloadkegg_pathway_listkegg_pathways_downloadkegg_picturekegg_processkinaseextralatin_nameligrecextralncrna_mrnaload_configload_dblogfilemirna_targetncbi_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_config_pathomnipath_for_cosmosomnipath_interactionsomnipath_load_configomnipath_logomnipath_logfileomnipath_msgomnipath_queryomnipath_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_downloadpathwayextrapivot_annotationspost_translationalpreppi_downloadpreppi_filterprint_bma_motif_esprint_bma_motif_vsprint_interactionsprint_path_esprint_path_vspubmed_openquery_inforamilowski_downloadramp_id_mapping_tableramp_id_typeramp_sqliteramp_tableramp_tablesread_logregnetwork_directionsregnetwork_downloadrelations_list_to_tablerelations_table_to_graphrelations_table_to_listremap_dorothea_downloadremap_filteredremap_tf_target_downloadreset_configresource_inforesourcesresources_colnameresources_insave_configset_loglevelshow_networksigned_ptmssimplify_intercell_networksmall_moleculestatic_tablestatic_tablesstitch_actionsstitch_linksstitch_networkstitch_remove_prefixessubnetworkswap_relationsswissprots_onlytf_mirnatf_targettfcensus_downloadtranscriptionaltranslate_idstranslate_ids_multitrembls_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:askpassbackportsbase64encbitbit64blobbslibcachemcellrangercheckmateclicliprcpp11crayoncurlDBIdigestdplyrevaluatefansifastmapfontawesomefsgenericsgluehighrhmshtmltoolshttrigraphjquerylibjsonliteknitrlaterlatticelifecycleloggerlubridatemagrittrMatrixmemoisemimeopensslpillarpkgconfigplogrprettyunitsprogresspurrrR.methodsS3R.ooR.utilsR6rappdirsRcppreadrreadxlrematchrlangrmarkdownRSQLitervestsassselectrstringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsvroomwithrxfunXMLxml2yamlzip

Building protein networks around drug-targets using OmnipathR

Attila Gabor, Alberto Valdeolivas, Julio Saez-Rodriguez

Rendered fromdrug_targets.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-17
Started: 2020-03-28

Building prior knowledge network (PKN) for COSMOS

Denes Turei

Rendered fromcosmos.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-22
Started: 2024-06-01

The database manager in OmnipathR

Denes Turei

Rendered fromdb_manager.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-29
Started: 2022-02-20

Resource specific interaction attributes

Denes Turei

Rendered fromextra_attrs.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-19
Started: 2022-02-15

OmniPath Bioconductor workshop

Denes Turei, Alberto Valdeolivas, Attila Gabor, Julio Saez-Rodriguez

Rendered frombioc_workshop.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-29
Started: 2021-03-16

OmnipathR: an R client for the OmniPath web service

Alberto Valdeolivas, Attila Gabor, Denes Turei, Julio Saez-Rodriguez

Rendered fromomnipath_intro.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-22
Started: 2020-10-02

Pathway construction

Denes Turei

Rendered frompaths.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-20
Started: 2021-08-04

Using NicheNet with OmnipathR

Denes Turei, Alberto Valdeolivas, Julio Saez-Rodriguez

Rendered fromnichenet.Rmdusingknitr::rmarkdownon Dec 18 2024.

Last update: 2024-08-17
Started: 2021-03-12

Readme and manuals

Help Manual

Help pageTopics
Default values for the package options.omnipathr_options_defaults
All UniProt ACs for one organismall_uniprot_acs
A table with all UniProt recordsall_uniprots
All ancestors in the ontology treeancestors
Network interactions with annotationsannotated_network
Annotation categories and resourcesannotation_categories
Retrieves a list of available resources in the annotations database of OmniPathannotation_resources get_annotation_resources
Protein and gene annotations from OmniPathannotations import_omnipath_annotations
Query the Ensembl BioMart web servicebiomart_query
Downloads all BioPlex interaction datasetsbioplex_all
Downloads the BioPlex HCT116 version 1.0 interaction datasetbioplex_hct116_1
Downloads the BioPlex version 1.0 interaction datasetbioplex1
Downloads the BioPlex version 2.0 interaction datasetbioplex2
Downloads the BioPlex version 3.0 interaction datasetbioplex3
BMA motifs from a sequence of edgesbma_motif_es
Prints a BMA motif to the screen from a sequence of nodes, which can be copy/pasted into the BMA canvasbma_motif_vs
Genome scale metabolic model by Wang et al. 2021chalmers_gem
Metabolite ID translation tables from Chalmers Sysbiochalmers_gem_id_mapping_table
Metabolite identifier type label used in Chalmers Sysbio GEMchalmers_gem_id_type
Metabolites from the Chalmers SysBio GEM (Wang et al., 2021)chalmers_gem_metabolites
Chalmers SysBio GEM in the form of gene-metabolite interactionschalmers_gem_network
GEM matlab file from Chalmers Sysbio (Wang et al., 2021)chalmers_gem_raw
Reactions from the Chalmers SysBio GEM (Wang et al., 2021)chalmers_gem_reactions
Common (English) names of organismscommon_name
Get all the molecular complexes for a given gene(s)complex_genes get_complex_genes
Retrieve a list of complex resources available in Omnipathcomplex_resources get_complex_resources
Protein complexes from OmniPathcomplexes import_omnipath_complexes
Retrieves the ConsensusPathDB networkconsensuspathdb_download
Downloads interaction data from ConsensusPathDBconsensuspathdb_raw_table
Acquire a cookie if necessarycookie
Prior knowledge network (PKN) for COSMOScosmos_pkn
Curated ligand-receptor interactionscurated_ligand_receptor_interactions
Statistics about literature curated ligand-receptor interactionscurated_ligrec_stats
Summary of the annotations and intercell database contentsdatabase_summary
Create a column with dataset names listeddatasets_one_column
All descendants in the ontology treedescendants
Ensembl dataset name from organismensembl_dataset
Identifier translation table from Ensemblensembl_id_mapping_table
Ensembl identifier type labelensembl_id_type
Ensembl identifiers of organismsensembl_name
Organism names and identifiers from Ensemblensembl_organisms
Table of Ensembl organismsensembl_organisms_raw
Orthologous gene pairs from Ensemblensembl_orthology
Converts a network to igraph object unless it is already oneensure_igraph
Enzyme-substrate graphenzsub_graph
Retrieves a list of enzyme-substrate resources available in OmniPathenzsub_resources get_enzsub_resources
Enzyme-substrate (PTM) relationships from OmniPathenzyme_substrate import_omnipath_enzsub
Interactions from the EVEX databaseevex_download
Show evidences for an interactionevidences
Possible values of an extra attributeextra_attr_values
Extra attribute names in an interaction data frameextra_attrs
New columns from extra attributesextra_attrs_to_cols
Filters OmniPath data by resourcesfilter_by_resource
Filter evidences by dataset, resource and licensefilter_evidences
Filter interactions by extra attribute valuesfilter_extra_attrs
Filter intercell annotationsfilter_intercell
Quality filter an intercell networkfilter_intercell_network
All paths between two groups of verticesfind_all_paths
Recreate interaction records from evidences columnsfrom_evidences
Access a built in databaseget_db
Access an ontology databaseget_ontology_db
Giant component of a graphgiant_component
Gene annotations from Gene Ontologygo_annot_download
GO slim gene annotationsgo_annot_slim
The Gene Ontology treego_ontology_download
Interaction data frame from igraph graph objectgraph_interaction
Downloads interactions from the Guide to Pharmacology databaseguide2pharma_download
Downloads a Harmonizome network datasetharmonizome_download
Tells if an interaction data frame has an extra_attrs columnhas_extra_attrs
Identifier translation table from HMDBhmdb_id_mapping_table
HMDB identifier type labelhmdb_id_type
Field names for the HMDB metabolite datasethmdb_metabolite_fields
Field names for the HMDB proteins datasethmdb_protein_fields
Download a HMDB XML file and process it into a tablehmdb_table
Orthology table for a pair of organismshomologene_download
Organisms in NCBI HomoloGenehomologene_organisms
Orthology data from NCBI HomoloGenehomologene_raw
Orthology table with UniProt IDshomologene_uniprot_orthology
Downloads protein annotations from Human Phenotype Ontologyhpo_download
Downloads TF-target interactions from HTRIdbhtridb_download
List available ID translation resourcesid_translation_resources
ID types and synonyms in identifier translationid_types
Downloads and preprocesses network data from InWeb InBioMapinbiomap_download
Downloads network data from InWeb InBioMapinbiomap_raw
Datasets in the OmniPath Interactions databaseinteraction_datasets
Build Omnipath interaction graphinteraction_graph
Interaction resources available in Omnipathget_interaction_resources interaction_resources
Interaction types in the OmniPath Interactions databaseinteraction_types
Cell-cell communication roles from OmniPathimport_omnipath_intercell intercell
Categories in the intercell database of OmniPathget_intercell_categories intercell_categories
Quality filter for intercell annotationsintercell_consensus_filter
Retrieves a list of the generic categories in the intercell database of OmniPathget_intercell_generic_categories intercell_generic_categories
Intercellular communication networkimport_intercell_network intercell_network
Retrieves a list of intercellular communication resources available in OmniPathget_intercell_resources intercell_resources
Full list of intercell categories and resourcesintercell_summary
Looks like an ontology IDis_ontology_id
Check for SwissProt IDsis_swissprot
Check for TrEMBL IDsis_trembl
Looks like a UniProt ID?is_uniprot
Information about a KEGG Pathwaykegg_info
Open a KEGG Pathway diagram in the browserkegg_open
Protein pathway annotationskegg_pathway_annotations
Download one KEGG pathwaykegg_pathway_download
List of KEGG pathwayskegg_pathway_list
Download the KEGG Pathways databasekegg_pathways_download
Download a pathway diagram as a picturekegg_picture
Interactions from KGMLkegg_process
Latin (scientific) names of organismslatin_name
Load a built in databaseload_db
NCBI Taxonomy IDs of organismsncbi_taxid
Construct a NicheNet ligand-target modelnichenet_build_model
Expression data from ligand-receptor perturbation experiments used by NicheNetnichenet_expression_data
Builds a NicheNet gene regulatory networknichenet_gr_network
NicheNet gene regulatory network from EVEXnichenet_gr_network_evex
NicheNet gene regulatory network from Harmonizomenichenet_gr_network_harmonizome
NicheNet gene regulatory network from HTRIdbnichenet_gr_network_htridb
Builds gene regulatory network for NicheNet using OmniPathnichenet_gr_network_omnipath
NicheNet gene regulatory network from PathwayCommonsnichenet_gr_network_pathwaycommons
NicheNet gene regulatory network from RegNetworknichenet_gr_network_regnetwork
NicheNet gene regulatory network from ReMapnichenet_gr_network_remap
NicheNet gene regulatory network from TRRUSTnichenet_gr_network_trrust
Calls the NicheNet ligand activity analysisnichenet_ligand_activities
Compiles a table with weighted ligand-target linksnichenet_ligand_target_links
Creates a NicheNet ligand-target matrixnichenet_ligand_target_matrix
Builds a NicheNet ligand-receptor networknichenet_lr_network
Ligand-receptor network from Guide to Pharmacologynichenet_lr_network_guide2pharma
Builds ligand-receptor network for NicheNet using OmniPathnichenet_lr_network_omnipath
Ligand-receptor network from Ramilowski 2015nichenet_lr_network_ramilowski
Executes the full NicheNet pipelinenichenet_main
Builds NicheNet network prior knowledgenichenet_networks
Optimizes NicheNet model parametersnichenet_optimization
Removes experiments with orphan ligandsnichenet_remove_orphan_ligands
Path to the current NicheNet results directorynichenet_results_dir
Builds a NicheNet signaling networknichenet_signaling_network
Builds signaling network for NicheNet using ConsensusPathDBnichenet_signaling_network_cpdb
NicheNet signaling network from EVEXnichenet_signaling_network_evex
NicheNet signaling network from Harmonizomenichenet_signaling_network_harmonizome
NicheNet signaling network from InWeb InBioMapnichenet_signaling_network_inbiomap
Builds signaling network for NicheNet using OmniPathnichenet_signaling_network_omnipath
NicheNet signaling network from PathwayCommonsnichenet_signaling_network_pathwaycommons
NicheNet signaling network from Vinayagamnichenet_signaling_network_vinayagam
Run the NicheNet pipeline with a little dummy networknichenet_test
Workarounds using NicheNet without attaching the packagenichenet_workarounds
Generic OBO parserobo_parser
Orthologous Matrix (OMA) codes of organismsoma_code
Organism identifiers from the Orthologous Matrixoma_organisms
Orthologous gene pairs between two organismsoma_pairwise
Orthologous pairs of gene symbols between two organismsoma_pairwise_genesymbols
Orthologous pairs between two organisms for ID types not supported by OMAoma_pairwise_translated
Keeps only the latest versions of complete downloadsomnipath_cache_autoclean
Removes the items from the cache directory which are unknown by the cache databaseomnipath_cache_clean
Removes the cache database entries without existing filesomnipath_cache_clean_db
Sets the download status to ready for a cache itemomnipath_cache_download_ready
Filters the versions from one cache recordomnipath_cache_filter_versions
Retrieves one item from the cache directoryomnipath_cache_get
Generates a hash which identifies an element in the cache databaseomnipath_cache_key
The latest or a new version of a cache recordomnipath_cache_latest_or_new
Finds the most recent version in a cache recordomnipath_cache_latest_version
Loads an R object from the cacheomnipath_cache_load
Moves an existing file into the cacheomnipath_cache_move_in
Removes contents from the cache directoryomnipath_cache_remove
Saves an R object to the cacheomnipath_cache_save
Searches for cache itemsomnipath_cache_search
Sets the file extension for a cache recordomnipath_cache_set_ext
Updates the status of an existing cache recordomnipath_cache_update_status
Permanently removes all the cache contentsomnipath_cache_wipe
Current config file path of OmnipathRconfig_path omnipath_config_path
OmniPath PPI for the COSMOS PKNomnipath_for_cosmos
Load the package configuration from a config fileload_config omnipath_load_config
Browse the current OmnipathR log fileomnipath_log read_log
Path to the current OmnipathR log filelogfile omnipath_logfile
Dispatch a message to the OmnipathR loggeromnipath_msg
Download data from the OmniPath web serviceomnipath_query
Save the current package configurationomnipath_save_config save_config
Change the cache directoryomnipath_set_cachedir
Sets the log level for the consoleomnipath_set_console_loglevel
Sets the log level for the logfileomnipath_set_logfile_loglevel
Sets the log level for the package loggeromnipath_set_loglevel set_loglevel
Built in database definitionsomnipath_show_db
Removes the lock file from the cache directoryomnipath_unlock_cache_db
Molecular interactions from OmniPathall_interactions collectri dorothea import_all_interactions import_dorothea_interactions import_kinaseextra_interactions import_ligrecextra_interactions import_lncrna_mrna_interactions import_mirnatarget_interactions import_omnipath_interactions import_pathwayextra_interactions import_post_translational_interactions import_small_molecule_protein_interactions import_tf_mirna_interactions import_tf_target_interactions import_transcriptional_interactions kinaseextra ligrecextra lncrna_mrna mirna_target omnipath omnipath-interactions omnipath_interactions pathwayextra post_translational small_molecule tf_mirna tf_target transcriptional
The OmnipathR packageOmnipathR-package OmnipathR
Recreate interaction data frame based on certain datasets and resourcesonly_from
Only ontology IDsontology_ensure_id
Only ontology term namesontology_ensure_name
Translate between ontology IDs and namesontology_name_id
Make sure the resource supports the organism and it has the IDorganism_for
Translate a column of identifiers by orthologous gene pairsorthology_translate_column
Interactions from PathwayCommonspathwaycommons_download
Converts annotation tables to a wide formatpivot_annotations
Interactions from PrePPIpreppi_download
Filter PrePPI interactions by scorespreppi_filter
Prints BMA motifs to the screen from a sequence of edgesprint_bma_motif_es
Prints BMA motifs to the screen from a sequence of nodesprint_bma_motif_vs
Print OmniPath interactionsprint_interactions
Prints network paths in an edge sequenceprint_path_es
Print networks paths given by node sequenceprint_path_vs
Open one or more PubMed articlespubmed_open
OmniPath query parametersquery_info
Downloads ligand-receptor interactions from Ramilowski et al. 2015ramilowski_download
Pairwise ID translation table from RaMP databaseramp_id_mapping_table
RaMP identifier type labelramp_id_type
Download and open RaMP database SQLiteramp_sqlite
Return table from RaMP databaseramp_table
List tables in RaMP databaseramp_tables
Transcription factor effects from RegNetworkregnetwork_directions
Interactions from RegNetworkregnetwork_download
Table from a nested list of ontology relationsrelations_list_to_table
Graph from a table of ontology relationsrelations_table_to_graph
Nested list from a table of ontology relationsrelations_table_to_list
Downloads TF-target interactions from ReMapremap_dorothea_download
Downloads TF-target interactions from ReMapremap_filtered
Downloads TF-target interactions from ReMapremap_tf_target_download
Restore the built-in default values of all config parameters of a packageomnipath_reset_config reset_config
OmniPath resource informationresource_info
Retrieve the available resources for a given query typeget_resources resources
Name of the column with the resourcesresources_colname
Collect resource names from a data frameresources_in
Visualize node neighborhood with SigmaJSshow_network
Causal effect enzyme-PTM interactionsget_signed_ptms signed_ptms
Simplify an intercell networksimplify_intercell_network
Retrieve a static table from OmniPathstatic_table
List the static tables available from OmniPathstatic_tables
Retrieve the STITCH actions datasetstitch_actions
Retrieve the STITCH links datasetstitch_links
Chemical-protein interactions from STITCHstitch_network
Remove the prefixes from STITCH identifiersstitch_remove_prefixes
Extract a custom subnetwork from a large networksubnetwork
Reverse the direction of ontology relationsswap_relations
Retain only SwissProt IDsswissprots_only
Downloads the list of transcription factors from TF censustfcensus_download
Translate gene, protein and small molecule identifierstranslate_ids
Translate gene, protein and small molecule identifiers from multiple columnstranslate_ids_multi
Retain only TrEMBL IDstrembls_only
Downloads TF-target interactions from TRRUSTtrrust_download
Creates an ID translation table from UniProt datauniprot_full_id_mapping_table
TrEMBL to SwissProt by gene namesuniprot_genesymbol_cleanup
ID translation data from UniProt ID Mappinguniprot_id_mapping_table
UniProt identifier type labeluniprot_id_type
ID types available in the UniProt ID Mapping serviceuniprot_idmapping_id_types
Unique intercellular interactionsunique_intercell_network
Separate evidences by direction and effect signunnest_evidences
UniProt Uploadlists identifier type labeluploadlists_id_type
Protein-protein interactions from Vinayagam 2011vinayagam_download
All nodes of a subtree starting from the selected nodeswalk_ontology_tree
Interaction records having certain extra attributeswith_extra_attrs
Interactions having referenceswith_references
Retrieves data from Zenodozenodo_download