Man pages for saezlab/OmnipathR
OmniPath web service client and more

all_uniprot_acsAll UniProt ACs for one organism
all_uniprotsA table with all UniProt records
ancestorsAll ancestors in the ontology tree
annotated_networkNetwork interactions with annotations
annotation_categoriesAnnotation categories and resources
annotation_resourcesRetrieves a list of available resources in the annotations...
annotationsProtein and gene annotations from OmniPath
biomart_queryQuery the Ensembl BioMart web service
bioplex1Downloads the BioPlex version 1.0 interaction dataset
bioplex2Downloads the BioPlex version 2.0 interaction dataset
bioplex3Downloads the BioPlex version 3.0 interaction dataset
bioplex_allDownloads all BioPlex interaction datasets
bioplex_hct116_1Downloads the BioPlex HCT116 version 1.0 interaction dataset
bma_motif_esBMA motifs from a sequence of edges
bma_motif_vsPrints a BMA motif to the screen from a sequence of nodes,...
chalmers_gemGenome scale metabolic model by Wang et al. 2021
chalmers_gem_id_mapping_tableMetabolite ID translation tables from Chalmers Sysbio
chalmers_gem_id_typeMetabolite identifier type label used in Chalmers Sysbio GEM
chalmers_gem_metabolitesMetabolites from the Chalmers SysBio GEM (Wang et al., 2021)
chalmers_gem_networkChalmers SysBio GEM in the form of gene-metabolite...
chalmers_gem_rawGEM matlab file from Chalmers Sysbio (Wang et al., 2021)
chalmers_gem_reactionsReactions from the Chalmers SysBio GEM (Wang et al., 2021)
common_nameCommon (English) names of organisms
complexesProtein complexes from OmniPath
complex_genesGet all the molecular complexes for a given gene(s)
complex_resourcesRetrieve a list of complex resources available in Omnipath
consensuspathdb_downloadRetrieves the ConsensusPathDB network
consensuspathdb_raw_tableDownloads interaction data from ConsensusPathDB
cookieAcquire a cookie if necessary
cosmos_pknPrior knowledge network (PKN) for COSMOS
curated_ligand_receptor_interactionsCurated ligand-receptor interactions
curated_ligrec_statsStatistics about literature curated ligand-receptor...
database_summarySummary of the annotations and intercell database contents
datasets_one_columnCreate a column with dataset names listed
descendantsAll descendants in the ontology tree
dot-omnipathr_options_defaultsDefault values for the package options
ensembl_datasetEnsembl dataset name from organism
ensembl_id_mapping_tableIdentifier translation table from Ensembl
ensembl_id_typeEnsembl identifier type label
ensembl_nameEnsembl identifiers of organisms
ensembl_organismsOrganism names and identifiers from Ensembl
ensembl_organisms_rawTable of Ensembl organisms
ensembl_orthologyOrthologous gene pairs from Ensembl
ensure_igraphConverts a network to igraph object unless it is already one
enzsub_graphEnzyme-substrate graph
enzsub_resourcesRetrieves a list of enzyme-substrate resources available in...
enzyme_substrateEnzyme-substrate (PTM) relationships from OmniPath
evex_downloadInteractions from the EVEX database
evidencesShow evidences for an interaction
extra_attrsExtra attribute names in an interaction data frame
extra_attrs_to_colsNew columns from extra attributes
extra_attr_valuesPossible values of an extra attribute
filter_by_resourceFilters OmniPath data by resources
filter_evidencesFilter evidences by dataset, resource and license
filter_extra_attrsFilter interactions by extra attribute values
filter_intercellFilter intercell annotations
filter_intercell_networkQuality filter an intercell network
find_all_pathsAll paths between two groups of vertices
from_evidencesRecreate interaction records from evidences columns
get_dbAccess a built in database
get_ontology_dbAccess an ontology database
giant_componentGiant component of a graph
go_annot_downloadGene annotations from Gene Ontology
go_annot_slimGO slim gene annotations
go_ontology_downloadThe Gene Ontology tree
graph_interactionInteraction data frame from igraph graph object
guide2pharma_downloadDownloads interactions from the Guide to Pharmacology...
harmonizome_downloadDownloads a Harmonizome network dataset
has_extra_attrsTells if an interaction data frame has an extra_attrs column
hmdb_id_mapping_tableIdentifier translation table from HMDB
hmdb_id_typeHMDB identifier type label
hmdb_metabolite_fieldsField names for the HMDB metabolite dataset
hmdb_protein_fieldsField names for the HMDB proteins dataset
hmdb_tableDownload a HMDB XML file and process it into a table
homologene_downloadOrthology table for a pair of organisms
homologene_organismsOrganisms in NCBI HomoloGene
homologene_rawOrthology data from NCBI HomoloGene
homologene_uniprot_orthologyOrthology table with UniProt IDs
hpo_downloadDownloads protein annotations from Human Phenotype Ontology
htridb_downloadDownloads TF-target interactions from HTRIdb
id_translation_resourcesList available ID translation resources
id_typesID types and synonyms in identifier translation
inbiomap_downloadDownloads and preprocesses network data from InWeb InBioMap
inbiomap_rawDownloads network data from InWeb InBioMap
interaction_datasetsDatasets in the OmniPath Interactions database
interaction_graphBuild Omnipath interaction graph
interaction_resourcesInteraction resources available in Omnipath
interaction_typesInteraction types in the OmniPath Interactions database
intercellCell-cell communication roles from OmniPath
intercell_categoriesCategories in the intercell database of OmniPath
intercell_consensus_filterQuality filter for intercell annotations
intercell_generic_categoriesRetrieves a list of the generic categories in the intercell...
intercell_networkIntercellular communication network
intercell_resourcesRetrieves a list of intercellular communication resources...
intercell_summaryFull list of intercell categories and resources
is_ontology_idLooks like an ontology ID
is_swissprotCheck for SwissProt IDs
is_tremblCheck for TrEMBL IDs
is_uniprotLooks like a UniProt ID?
kegg_infoInformation about a KEGG Pathway
kegg_openOpen a KEGG Pathway diagram in the browser
kegg_pathway_annotationsProtein pathway annotations
kegg_pathway_downloadDownload one KEGG pathway
kegg_pathway_listList of KEGG pathways
kegg_pathways_downloadDownload the KEGG Pathways database
kegg_pictureDownload a pathway diagram as a picture
kegg_processInteractions from KGML
latin_nameLatin (scientific) names of organisms
load_dbLoad a built in database
ncbi_taxidNCBI Taxonomy IDs of organisms
nichenet_build_modelConstruct a NicheNet ligand-target model
nichenet_expression_dataExpression data from ligand-receptor perturbation experiments...
nichenet_gr_networkBuilds a NicheNet gene regulatory network
nichenet_gr_network_evexNicheNet gene regulatory network from EVEX
nichenet_gr_network_harmonizomeNicheNet gene regulatory network from Harmonizome
nichenet_gr_network_htridbNicheNet gene regulatory network from HTRIdb
nichenet_gr_network_omnipathBuilds gene regulatory network for NicheNet using OmniPath
nichenet_gr_network_pathwaycommonsNicheNet gene regulatory network from PathwayCommons
nichenet_gr_network_regnetworkNicheNet gene regulatory network from RegNetwork
nichenet_gr_network_remapNicheNet gene regulatory network from ReMap
nichenet_gr_network_trrustNicheNet gene regulatory network from TRRUST
nichenet_ligand_activitiesCalls the NicheNet ligand activity analysis
nichenet_ligand_target_linksCompiles a table with weighted ligand-target links
nichenet_ligand_target_matrixCreates a NicheNet ligand-target matrix
nichenet_lr_networkBuilds a NicheNet ligand-receptor network
nichenet_lr_network_guide2pharmaLigand-receptor network from Guide to Pharmacology
nichenet_lr_network_omnipathBuilds ligand-receptor network for NicheNet using OmniPath
nichenet_lr_network_ramilowskiLigand-receptor network from Ramilowski 2015
nichenet_mainExecutes the full NicheNet pipeline
nichenet_networksBuilds NicheNet network prior knowledge
nichenet_optimizationOptimizes NicheNet model parameters
nichenet_remove_orphan_ligandsRemoves experiments with orphan ligands
nichenet_results_dirPath to the current NicheNet results directory
nichenet_signaling_networkBuilds a NicheNet signaling network
nichenet_signaling_network_cpdbBuilds signaling network for NicheNet using ConsensusPathDB
nichenet_signaling_network_evexNicheNet signaling network from EVEX
nichenet_signaling_network_harmonizomeNicheNet signaling network from Harmonizome
nichenet_signaling_network_inbiomapNicheNet signaling network from InWeb InBioMap
nichenet_signaling_network_omnipathBuilds signaling network for NicheNet using OmniPath
nichenet_signaling_network_pathwaycommonsNicheNet signaling network from PathwayCommons
nichenet_signaling_network_vinayagamNicheNet signaling network from Vinayagam
nichenet_testRun the NicheNet pipeline with a little dummy network
nichenet_workaroundsWorkarounds using NicheNet without attaching the package
obo_parserGeneric OBO parser
oma_codeOrthologous Matrix (OMA) codes of organisms
oma_organismsOrganism identifiers from the Orthologous Matrix
oma_pairwiseOrthologous gene pairs between two organisms
oma_pairwise_genesymbolsOrthologous pairs of gene symbols between two organisms
oma_pairwise_translatedOrthologous pairs between two organisms for ID types not...
omnipath_cache_autocleanKeeps only the latest versions of complete downloads
omnipath_cache_cleanRemoves the items from the cache directory which are unknown...
omnipath_cache_clean_dbRemoves the cache database entries without existing files
omnipath_cache_download_readySets the download status to ready for a cache item
omnipath_cache_filter_versionsFilters the versions from one cache record
omnipath_cache_getRetrieves one item from the cache directory
omnipath_cache_keyGenerates a hash which identifies an element in the cache...
omnipath_cache_latest_or_newThe latest or a new version of a cache record
omnipath_cache_latest_versionFinds the most recent version in a cache record
omnipath_cache_loadLoads an R object from the cache
omnipath_cache_move_inMoves an existing file into the cache
omnipath_cache_removeRemoves contents from the cache directory
omnipath_cache_saveSaves an R object to the cache
omnipath_cache_searchSearches for cache items
omnipath_cache_set_extSets the file extension for a cache record
omnipath_cache_update_statusUpdates the status of an existing cache record
omnipath_cache_wipePermanently removes all the cache contents
omnipath_config_pathCurrent config file path of OmnipathR
omnipath_for_cosmosOmniPath PPI for the COSMOS PKN
omnipath-interactionsMolecular interactions from OmniPath
omnipath_load_configLoad the package configuration from a config file
omnipath_logBrowse the current OmnipathR log file
omnipath_logfilePath to the current OmnipathR log file
omnipath_msgDispatch a message to the OmnipathR logger
omnipath_queryDownload data from the OmniPath web service
OmnipathRThe OmnipathR package
omnipath_reset_configRestore the built-in default values of all config parameters...
omnipath_save_configSave the current package configuration
omnipath_set_cachedirChange the cache directory
omnipath_set_console_loglevelSets the log level for the console
omnipath_set_logfile_loglevelSets the log level for the logfile
omnipath_set_loglevelSets the log level for the package logger
omnipath_show_dbBuilt in database definitions
omnipath_unlock_cache_dbRemoves the lock file from the cache directory
only_fromRecreate interaction data frame based on certain datasets and...
ontology_ensure_idOnly ontology IDs
ontology_ensure_nameOnly ontology term names
ontology_name_idTranslate between ontology IDs and names
organism_forMake sure the resource supports the organism and it has the...
orthology_translate_columnTranslate a column of identifiers by orthologous gene pairs
pathwaycommons_downloadInteractions from PathwayCommons
pivot_annotationsConverts annotation tables to a wide format
preppi_downloadInteractions from PrePPI
preppi_filterFilter PrePPI interactions by scores
print_bma_motif_esPrints BMA motifs to the screen from a sequence of edges
print_bma_motif_vsPrints BMA motifs to the screen from a sequence of nodes
print_interactionsPrint OmniPath interactions
print_path_esPrints network paths in an edge sequence
print_path_vsPrint networks paths given by node sequence
pubmed_openOpen one or more PubMed articles
query_infoOmniPath query parameters
ramilowski_downloadDownloads ligand-receptor interactions from Ramilowski et al....
ramp_id_mapping_tablePairwise ID translation table from RaMP database
ramp_id_typeRaMP identifier type label
ramp_sqliteDownload and open RaMP database SQLite
ramp_tableReturn table from RaMP database
ramp_tablesList tables in RaMP database
regnetwork_directionsTranscription factor effects from RegNetwork
regnetwork_downloadInteractions from RegNetwork
relations_list_to_tableTable from a nested list of ontology relations
relations_table_to_graphGraph from a table of ontology relations
relations_table_to_listNested list from a table of ontology relations
remap_dorothea_downloadDownloads TF-target interactions from ReMap
remap_filteredDownloads TF-target interactions from ReMap
remap_tf_target_downloadDownloads TF-target interactions from ReMap
resource_infoOmniPath resource information
resourcesRetrieve the available resources for a given query type
resources_colnameName of the column with the resources
resources_inCollect resource names from a data frame
show_networkVisualize node neighborhood with SigmaJS
signed_ptmsCausal effect enzyme-PTM interactions
simplify_intercell_networkSimplify an intercell network
static_tableRetrieve a static table from OmniPath
static_tablesList the static tables available from OmniPath
stitch_actionsRetrieve the STITCH actions dataset
stitch_linksRetrieve the STITCH links dataset
stitch_networkChemical-protein interactions from STITCH
stitch_remove_prefixesRemove the prefixes from STITCH identifiers
subnetworkExtract a custom subnetwork from a large network
swap_relationsReverse the direction of ontology relations
swissprots_onlyRetain only SwissProt IDs
tfcensus_downloadDownloads the list of transcription factors from TF census
translate_idsTranslate gene, protein and small molecule identifiers
translate_ids_multiTranslate gene, protein and small molecule identifiers from...
trembls_onlyRetain only TrEMBL IDs
trrust_downloadDownloads TF-target interactions from TRRUST
uniprot_full_id_mapping_tableCreates an ID translation table from UniProt data
uniprot_genesymbol_cleanupTrEMBL to SwissProt by gene names
uniprot_idmapping_id_typesID types available in the UniProt ID Mapping service
uniprot_id_mapping_tableID translation data from UniProt ID Mapping
uniprot_id_typeUniProt identifier type label
unique_intercell_networkUnique intercellular interactions
unnest_evidencesSeparate evidences by direction and effect sign
uploadlists_id_typeUniProt Uploadlists identifier type label
vinayagam_downloadProtein-protein interactions from Vinayagam 2011
walk_ontology_treeAll nodes of a subtree starting from the selected nodes
with_extra_attrsInteraction records having certain extra attributes
with_referencesInteractions having references
zenodo_downloadRetrieves data from Zenodo
saezlab/OmnipathR documentation built on Oct. 16, 2024, 11:49 a.m.