Package index • OmnipathR

All functions

OmnipathR-package OmnipathR: The OmnipathR package

all_uniprot_acs(): All UniProt ACs for one organism

all_uniprots(): A table with all UniProt records

ambiguity(): Inspect the ambiguity of a mapping

ancestors(): All ancestors in the ontology tree

annotated_network(): Network interactions with annotations

annotation_categories(): Annotation categories and resources

annotation_resources(): Retrieves a list of available resources in the annotations database of OmniPath

annotations(): Protein and gene annotations from OmniPath

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

chalmers_gem(): Genome scale metabolic model by Wang et al. 2021

chalmers_gem_id_mapping_table(): Metabolite ID translation tables from Chalmers Sysbio

chalmers_gem_id_type(): Metabolite identifier type label used in Chalmers Sysbio GEM

chalmers_gem_metabolites(): Metabolites from the Chalmers SysBio GEM (Wang et al., 2021)

chalmers_gem_network(): Chalmers SysBio GEM in the form of gene-metabolite interactions

chalmers_gem_raw(): GEM matlab file from Chalmers Sysbio (Wang et al., 2021)

chalmers_gem_reactions(): Reactions from the Chalmers SysBio GEM (Wang et al., 2021)

common_name(): Common (English) names of organisms

complex_genes(): Get all the molecular complexes for a given gene(s)

complex_resources(): Retrieve a list of complex resources available in Omnipath

complexes(): Protein complexes from OmniPath

consensuspathdb_download(): Retrieves the ConsensusPathDB network

consensuspathdb_raw_table(): Downloads interaction data from ConsensusPathDB

cosmos_pkn(): Prior knowledge network (PKN) for COSMOS

curated_ligand_receptor_interactions(): Curated ligand-receptor interactions

curated_ligrec_stats(): Statistics about literature curated ligand-receptor interactions

database_summary(): Summary of the annotations and intercell database contents

datasets_one_column(): Create a column with dataset names listed

descendants(): All descendants in the ontology tree

.omnipathr_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

ensure_igraph(): Converts a network to igraph object unless it is already one

enzsub_graph(): Enzyme-substrate graph

enzsub_resources(): Retrieves a list of enzyme-substrate resources available in OmniPath

enzyme_substrate(): Enzyme-substrate (PTM) relationships from OmniPath

evex_download(): Interactions from the EVEX database

evidences(): Show evidences for an interaction

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_evidences(): Filter evidences by dataset, resource and license

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

from_evidences(): Recreate interaction records from evidences columns

get_db(): Access a built in database

get_ontology_db(): Access an ontology database

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

graph_interaction(): Interaction data frame from igraph graph object

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

hmdb_id_mapping_table(): Identifier translation table from HMDB

hmdb_id_type(): HMDB identifier type label

hmdb_metabolite_fields(): Field names for the HMDB metabolite dataset

hmdb_protein_fields(): Field names for the HMDB proteins dataset

hmdb_table(): Download a HMDB XML file and process it into a table

homologene_download(): Orthology table for a pair of organisms

homologene_organisms(): Organisms in NCBI HomoloGene

homologene_raw(): Orthology data from NCBI HomoloGene

homologene_uniprot_orthology(): Orthology table with UniProt IDs

hpo_download(): Downloads protein annotations from Human Phenotype Ontology

htridb_download(): Downloads TF-target interactions from HTRIdb

id_translation_resources(): List available ID translation resources

id_types(): ID types and synonyms in identifier translation

inbiomap_download(): Downloads and preprocesses network data from InWeb InBioMap

inbiomap_raw(): Downloads network data from InWeb InBioMap

interaction_datasets(): Datasets in the OmniPath Interactions database

interaction_graph(): Build Omnipath interaction graph

interaction_resources(): Interaction resources available in Omnipath

interaction_types(): Interaction types in the OmniPath Interactions database

intercell(): Cell-cell communication roles from OmniPath

intercell_categories(): Categories in the intercell database of OmniPath

intercell_consensus_filter(): Quality filter for intercell annotations

intercell_generic_categories(): Retrieves a list of the generic categories in the intercell database of OmniPath

intercell_network(): Intercellular communication network

intercell_resources(): Retrieves a list of intercellular communication resources available in OmniPath

intercell_summary(): Full list of intercell categories and resources

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_api_templates(): List of templates in the KEGG REST API

kegg_conv(): Convert KEGG identifiers to/from outside identifiers

kegg_databases(): List of databases (endpoints) in the KEGG REST API

kegg_ddi(): Find adverse drug-drug interactions in KEGG

kegg_find(): Find entries in KEGG with matching query keyword or other query data

kegg_info(): Information about a KEGG Pathway

kegg_link(): Find related KEGG entries by using database cross-references

kegg_list(): Obtain a list of KEGG entry identifiers and associated names

kegg_open(): Open a KEGG Pathway diagram in the browser

kegg_operations(): List of operations in the KEGG REST API

kegg_organism_codes(): All 3 letter organism code from KEGG

kegg_organisms(): List of organisms in KEGG

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

kegg_query(): Compile a query for the KEGG REST API

kegg_request(): Perform a KEGG REST API request

kegg_rm_prefix(): Remove prefix from KEGG foreign database identifiers

latin_name(): Latin (scientific) names of organisms

load_db(): Load a built in database

metalinksdb_sqlite(): Open MetalinksDB as an SQLite3 connection

metalinksdb_table(): A table from MetalinksDB

metalinksdb_tables(): List tables in MetalinksDB

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

oma_code(): Orthologous Matrix (OMA) codes of organisms

oma_organisms(): Organism identifiers from the Orthologous Matrix

oma_pairwise(): Orthologous gene pairs between two organisms

oma_pairwise_genesymbols(): Orthologous pairs of gene symbols between two organisms

oma_pairwise_translated(): Orthologous pairs between two organisms for ID types not supported by OMA

omnipath_interactions() omnipath() pathwayextra() kinaseextra() ligrecextra() post_translational() dorothea() tf_target() transcriptional() collectri() mirna_target() tf_mirna() lncrna_mrna() small_molecule() all_interactions(): Molecular interactions from OmniPath

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_config_path() config_path(): Current config file path of OmnipathR

omnipath_for_cosmos(): OmniPath PPI for the COSMOS PKN

omnipath_load_config() load_config(): Load the package configuration from a config file

omnipath_log() read_log(): Browse the current OmnipathR log file

omnipath_logfile() logfile(): Path to the current OmnipathR log file

omnipath_msg(): Dispatch a message to the OmnipathR logger

omnipath_query(): Download data from the OmniPath web service

reset_config() omnipath_reset_config(): Restore the built-in default values of all config parameters of a package

omnipath_save_config() 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() 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

only_from(): Recreate interaction data frame based on certain datasets and resources

ontology_ensure_id(): Only ontology IDs

ontology_ensure_name(): Only ontology term names

ontology_name_id(): Translate between ontology IDs and names

organism_for(): Make sure the resource supports the organism and it has the ID

orthology_translate_column(): Translate a column of identifiers by orthologous gene pairs

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

query_info(): OmniPath query parameters

ramilowski_download(): Downloads ligand-receptor interactions from Ramilowski et al. 2015

ramp_id_mapping_table(): Pairwise ID translation table from RaMP database

ramp_id_type(): RaMP identifier type label

ramp_sqlite(): Download and open RaMP database SQLite

ramp_table(): Return table from RaMP database

ramp_tables(): List tables in RaMP database

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

resource_info(): OmniPath resource information

resources(): Retrieve the available resources for a given query type

resources_colname(): Name of the column with the resources

resources_in(): Collect resource names from a data frame

show_network(): Visualize node neighborhood with SigmaJS

signed_ptms(): Causal effect enzyme-PTM interactions

simplify_intercell_network(): Simplify an intercell network

static_table(): Retrieve a static table from OmniPath

static_tables(): List the static tables available from OmniPath

stitch_actions(): Retrieve the STITCH actions dataset

stitch_links(): Retrieve the STITCH links dataset

stitch_network(): Chemical-protein interactions from STITCH

stitch_remove_prefixes(): Remove the prefixes from STITCH identifiers

subnetwork(): Extract a custom subnetwork from a large 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, protein and small molecule identifiers

translate_ids_multi(): Translate gene, protein and small molecule identifiers from multiple columns

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 ID Mapping

uniprot_id_type(): UniProt identifier type label

uniprot_idmapping_id_types(): ID types available in the UniProt ID Mapping service

unique_intercell_network(): Unique intercellular interactions

unnest_evidences(): Separate evidences by direction and effect sign

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