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All functions

OmnipathR
The OmnipathR package
all_uniprot_acs()
All UniProt ACs for one organism
all_uniprots()
A table with all UniProt records
ancestors()
All ancestors in the ontology tree
annotated_network()
Network interactions with annotations
annotation_categories()
Annotation categories and resources
biomart_query()
Query the Ensembl BioMart web service
bioplex1()
Downloads the BioPlex version 1.0 interaction dataset
bioplex2()
Downloads the BioPlex version 2.0 interaction dataset
bioplex3()
Downloads the BioPlex version 3.0 interaction dataset
bioplex_all()
Downloads all BioPlex interaction datasets
bioplex_hct116_1()
Downloads the BioPlex HCT116 version 1.0 interaction dataset
bma_motif_es()
BMA motifs from a sequence of edges
bma_motif_vs()
Prints a BMA motif to the screen from a sequence of nodes, which can be copy/pasted into the BMA canvas
common_name()
Common (English) names of organisms
consensuspathdb_download()
Retrieves the ConsensusPathDB network
consensuspathdb_raw_table()
Downloads interaction data from ConsensusPathDB
curated_ligand_receptor_interactions()
Curated ligand-receptor interactions
curated_ligrec_stats()
Statistics about literature curated ligand-receptor interactions
descendants()
All descendants in the ontology tree
.omnipath_options_defaults
Default values for the package options
ensembl_dataset()
Ensembl dataset name from organism
ensembl_id_mapping_table()
Identifier translation table from Ensembl
ensembl_id_type()
Ensembl identifier type label
ensembl_name()
Ensembl identifiers of organisms
ensembl_organisms()
Organism names and identifiers from Ensembl
ensembl_organisms_raw()
Table of Ensembl organisms
ensembl_orthology()
Orthologous gene pairs from Ensembl
enzsub_graph()
Enzyme-substrate graph
evex_download()
Interactions from the EVEX database
extra_attr_values()
Possible values of an extra attribute
extra_attrs()
Extra attribute names in an interaction data frame
extra_attrs_to_cols()
New columns from extra attributes
filter_by_resource()
Filters OmniPath data by resources
filter_extra_attrs()
Filter interactions by extra attribute values
filter_intercell()
Filter intercell annotations
filter_intercell_network()
Quality filter an intercell network
find_all_paths()
All paths between two groups of vertices
get_annotation_resources()
Retrieves a list of available resources in the annotations database of OmniPath
get_complex_genes()
Get all the molecular complexes for a given gene(s)
get_complex_resources()
Retrieve a list of complex resources available in Omnipath
get_db()
Access a built in database
get_enzsub_resources()
Retrieves a list of enzyme-substrate resources available in OmniPath
get_interaction_resources()
Retrieve a list of interaction resources available in Omnipath
get_intercell_categories()
Categories in the intercell database of OmniPath
get_intercell_generic_categories()
Retrieves a list of the generic categories in the intercell database of OmniPath
get_intercell_resources()
Retrieves a list of intercellular communication resources available in OmniPath
get_ontology_db()
Access an ontology database
get_resources()
Retrieve the available resources for a given query type
get_signed_ptms()
Signs for enzyme-substrate interactions
giant_component()
Giant component of a graph
go_annot_download()
Gene annotations from Gene Ontology
go_annot_slim()
GO slim gene annotations
go_ontology_download()
The Gene Ontology tree
guide2pharma_download()
Downloads interactions from the Guide to Pharmacology database
harmonizome_download()
Downloads a Harmonizome network dataset
has_extra_attrs()
Tells if an interaction data frame has an extra_attrs column
homologene_download()
Orthology table for a pair of organisms
homologene_raw()
Orthology data from NCBI HomoloGene
homologene_uniprot_orthology()
Orthology table with UniProt IDs
homology_translate()
Homology translation
hpo_download()
Downloads protein annotations from Human Phenotype Ontology
htridb_download()
Downloads TF-target interactions from HTRIdb
import_all_interactions() import_AllInteractions()
Imports all interaction datasets available in OmniPath
import_dorothea_interactions()
From the OmniPath webservice imports interactions from the DoRothEA dataset
import_intercell_network()
Intercellular communication network
import_kinaseextra_interactions()
Imports interactions from the `kinase extra` dataset of OmniPath
import_ligrecextra_interactions()
Imports interactions from the `ligrec extra` dataset of OmniPath
import_lncrna_mrna_interactions()
Imports interactions from the lncRNA-mRNA dataset of OmniPath
import_mirnatarget_interactions()
Imports interactions from the miRNA-target dataset of OmniPath
import_omnipath_annotations()
Imports annotations from OmniPath
import_omnipath_complexes()
Imports protein complexes from OmniPath
import_omnipath_enzsub()
Imports enzyme-substrate relationships from OmniPath
import_omnipath_interactions()
Imports interactions from the `omnipath` dataset of Omnipath
import_omnipath_intercell()
Imports OmniPath intercell annotations
import_pathwayextra_interactions()
Imports interactions from the `pathway extra` dataset of Omnipath
import_post_translational_interactions()
All post-translational interactions from OmniPath
import_small_molecule_protein_interactions()
Interactions from the small molecule-protein dataset of OmniPath
import_tf_mirna_interactions()
Imports interactions from the TF-miRNA dataset of OmniPath
import_tf_target_interactions()
Imports interactions from the TF-target dataset of OmniPath
import_transcriptional_interactions()
Imports all TF-target interactions from OmniPath
inbiomap_download()
Downloads and preprocesses network data from InWeb InBioMap
inbiomap_raw()
Downloads network data from InWeb InBioMap
interaction_graph()
Build Omnipath interaction graph
intercell_categories()
Full list of intercell categories and resources
intercell_consensus_filter()
Quality filter for intercell annotations
is_ontology_id()
Looks like an ontology ID
is_swissprot()
Check for SwissProt IDs
is_trembl()
Check for TrEMBL IDs
is_uniprot()
Looks like a UniProt ID?
kegg_info()
Information about a KEGG Pathway
kegg_open()
Open a KEGG Pathway diagram in the browser
kegg_pathway_annotations()
Protein pathway annotations
kegg_pathway_download()
Download one KEGG pathway
kegg_pathway_list()
List of KEGG pathways
kegg_pathways_download()
Download the KEGG Pathways database
kegg_picture()
Download a pathway diagram as a picture
kegg_process()
Interactions from KGML
latin_name()
Latin (scientific) names of organisms
load_db()
Load a built in database
ncbi_taxid()
NCBI Taxonomy IDs of organisms
nichenet_build_model()
Construct a NicheNet ligand-target model
nichenet_expression_data()
Expression data from ligand-receptor perturbation experiments used by NicheNet
nichenet_gr_network()
Builds a NicheNet gene regulatory network
nichenet_gr_network_evex()
NicheNet gene regulatory network from EVEX
nichenet_gr_network_harmonizome()
NicheNet gene regulatory network from Harmonizome
nichenet_gr_network_htridb()
NicheNet gene regulatory network from HTRIdb
nichenet_gr_network_omnipath()
Builds gene regulatory network for NicheNet using OmniPath
nichenet_gr_network_pathwaycommons()
NicheNet gene regulatory network from PathwayCommons
nichenet_gr_network_regnetwork()
NicheNet gene regulatory network from RegNetwork
nichenet_gr_network_remap()
NicheNet gene regulatory network from ReMap
nichenet_gr_network_trrust()
NicheNet gene regulatory network from TRRUST
nichenet_ligand_activities()
Calls the NicheNet ligand activity analysis
nichenet_ligand_target_links()
Compiles a table with weighted ligand-target links
nichenet_ligand_target_matrix()
Creates a NicheNet ligand-target matrix
nichenet_lr_network()
Builds a NicheNet ligand-receptor network
nichenet_lr_network_guide2pharma()
Ligand-receptor network from Guide to Pharmacology
nichenet_lr_network_omnipath()
Builds ligand-receptor network for NicheNet using OmniPath
nichenet_lr_network_ramilowski()
Ligand-receptor network from Ramilowski 2015
nichenet_main()
Executes the full NicheNet pipeline
nichenet_networks()
Builds NicheNet network prior knowledge
nichenet_optimization()
Optimizes NicheNet model parameters
nichenet_remove_orphan_ligands()
Removes experiments with orphan ligands
nichenet_results_dir()
Path to the current NicheNet results directory
nichenet_signaling_network()
Builds a NicheNet signaling network
nichenet_signaling_network_cpdb()
Builds signaling network for NicheNet using ConsensusPathDB
nichenet_signaling_network_evex()
NicheNet signaling network from EVEX
nichenet_signaling_network_harmonizome()
NicheNet signaling network from Harmonizome
nichenet_signaling_network_inbiomap()
NicheNet signaling network from InWeb InBioMap
nichenet_signaling_network_omnipath()
Builds signaling network for NicheNet using OmniPath
nichenet_signaling_network_pathwaycommons()
NicheNet signaling network from PathwayCommons
nichenet_signaling_network_vinayagam()
NicheNet signaling network from Vinayagam
nichenet_test()
Run the NicheNet pipeline with a little dummy network
nichenet_workarounds()
Workarounds using NicheNet without attaching the package
obo_parser()
Generic OBO parser
omnipath_cache_autoclean()
Keeps only the latest versions of complete downloads
omnipath_cache_clean()
Removes the items from the cache directory which are unknown by the cache database
omnipath_cache_clean_db()
Removes the cache database entries without existing files
omnipath_cache_download_ready()
Sets the download status to ready for a cache item
omnipath_cache_filter_versions()
Filters the versions from one cache record
omnipath_cache_get()
Retrieves one item from the cache directory
omnipath_cache_key()
Generates a hash which identifies an element in the cache database
omnipath_cache_latest_or_new()
The latest or a new version of a cache record
omnipath_cache_latest_version()
Finds the most recent version in a cache record
omnipath_cache_load()
Loads an R object from the cache
omnipath_cache_move_in()
Moves an existing file into the cache
omnipath_cache_remove()
Removes contents from the cache directory
omnipath_cache_save()
Saves an R object to the cache
omnipath_cache_search()
Searches for cache items
omnipath_cache_set_ext()
Sets the file extension for a cache record
omnipath_cache_update_status()
Updates the status of an existing cache record
omnipath_cache_wipe()
Permanently removes all the cache contents
omnipath_get_config_path()
Current config file path
omnipath_load_config()
Load the package configuration from a config file
omnipath_log()
Browse the current OmnipathR log file
omnipath_logfile()
Path to the current OmnipathR log file
omnipath_msg()
Dispatch a message to the OmnipathR logger
omnipath_reset_config()
Restores the built-in default values of all config parameters
omnipath_save_config()
Save the current package configuration
omnipath_set_cachedir()
Change the cache directory
omnipath_set_console_loglevel()
Sets the log level for the console
omnipath_set_logfile_loglevel()
Sets the log level for the logfile
omnipath_set_loglevel()
Sets the log level for the package logger
omnipath_show_db()
Built in database definitions
omnipath_unlock_cache_db()
Removes the lock file from the cache directory
ontology_ensure_id()
Only ontology IDs
ontology_ensure_name()
Only ontology term names
ontology_name_id()
Translate between ontology IDs and names
pathwaycommons_download()
Interactions from PathwayCommons
pivot_annotations()
Converts annotation tables to a wide format
preppi_download()
Interactions from PrePPI
preppi_filter()
Filter PrePPI interactions by scores
print_bma_motif_es()
Prints BMA motifs to the screen from a sequence of edges
print_bma_motif_vs()
Prints BMA motifs to the screen from a sequence of nodes
print_interactions()
Print OmniPath interactions
print_path_es()
Prints network paths in an edge sequence
print_path_vs()
Print networks paths given by node sequence
pubmed_open()
Open one or more PubMed articles
ramilowski_download()
Downloads ligand-receptor interactions from Ramilowski et al. 2015
regnetwork_directions()
Transcription factor effects from RegNetwork
regnetwork_download()
Interactions from RegNetwork
relations_list_to_table()
Table from a nested list of ontology relations
relations_table_to_graph()
Graph from a table of ontology relations
relations_table_to_list()
Nested list from a table of ontology relations
remap_dorothea_download()
Downloads TF-target interactions from ReMap
remap_filtered()
Downloads TF-target interactions from ReMap
remap_tf_target_download()
Downloads TF-target interactions from ReMap
resources_colname()
Name of the column with the resources
simplify_intercell_network()
Simplify an intercell network
swap_relations()
Reverse the direction of ontology relations
swissprots_only()
Retain only SwissProt IDs
tfcensus_download()
Downloads the list of transcription factors from TF census
translate_ids()
Translate gene and protein identifiers
trembls_only()
Retain only TrEMBL IDs
trrust_download()
Downloads TF-target interactions from TRRUST
uniprot_full_id_mapping_table()
Creates an ID translation table from UniProt data
uniprot_genesymbol_cleanup()
TrEMBL to SwissProt by gene names
uniprot_id_mapping_table()
ID translation data from UniProt Uploadlists
uniprot_id_type()
UniProt identifier type label
unique_intercell_network()
Unique intercellular interactions
uploadlists_id_type()
UniProt Uploadlists identifier type label
vinayagam_download()
Protein-protein interactions from Vinayagam 2011
walk_ontology_tree()
All nodes of a subtree starting from the selected nodes
with_extra_attrs()
Interaction records having certain extra attributes
with_references()
Interactions having references
zenodo_download()
Retrieves data from Zenodo