OmniPath web service client and more


[Up] [Top]

Documentation for package ‘OmnipathR’ version 3.17.0

Help Pages

A B C D E F G H I K L M N O P Q R S T U V W Z misc

OmnipathR-package The OmnipathR package

-- A --

all_interactions Molecular interactions from OmniPath
all_uniprots A table with all UniProt records
all_uniprot_acs All UniProt ACs for one organism
ambiguity Inspect the ambiguity of a mapping
ancestors All ancestors in the ontology tree
annotated_network Network interactions with annotations
annotations Protein and gene annotations from OmniPath
annotation_categories Annotation categories and resources
annotation_resources Retrieves a list of available resources in the annotations database of OmniPath

-- B --

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

-- C --

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)
collectri Molecular interactions from OmniPath
common_name Common (English) names of organisms
complexes Protein complexes from OmniPath
complex_genes Get all the molecular complexes for a given gene(s)
complex_resources Retrieve a list of complex resources available in Omnipath
config_path Current config file path of OmnipathR
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

-- D --

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
dorothea Molecular interactions from OmniPath

-- E --

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_attrs Extra attribute names in an interaction data frame
extra_attrs_to_cols New columns from extra attributes
extra_attr_values Possible values of an extra attribute

-- F --

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

-- G --

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 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 Causal effect enzyme-PTM 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
graph_interaction Interaction data frame from igraph graph object
guide2pharma_download Downloads interactions from the Guide to Pharmacology database

-- H --

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

-- I --

id_translation_resources List available ID translation resources
id_types ID types and synonyms in identifier translation
import_all_interactions Molecular interactions from OmniPath
import_dorothea_interactions Molecular interactions from OmniPath
import_intercell_network Intercellular communication network
import_kinaseextra_interactions Molecular interactions from OmniPath
import_ligrecextra_interactions Molecular interactions from OmniPath
import_lncrna_mrna_interactions Molecular interactions from OmniPath
import_mirnatarget_interactions Molecular interactions from OmniPath
import_omnipath_annotations Protein and gene annotations from OmniPath
import_omnipath_complexes Protein complexes from OmniPath
import_omnipath_enzsub Enzyme-substrate (PTM) relationships from OmniPath
import_omnipath_interactions Molecular interactions from OmniPath
import_omnipath_intercell Cell-cell communication roles from OmniPath
import_pathwayextra_interactions Molecular interactions from OmniPath
import_post_translational_interactions Molecular interactions from OmniPath
import_small_molecule_protein_interactions Molecular interactions from OmniPath
import_tf_mirna_interactions Molecular interactions from OmniPath
import_tf_target_interactions Molecular interactions from OmniPath
import_transcriptional_interactions Molecular interactions from OmniPath
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?

-- K --

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_organisms List of organisms in KEGG
kegg_organism_codes All 3 letter organism code from KEGG
kegg_pathways_download Download the KEGG Pathways database
kegg_pathway_annotations Protein pathway annotations
kegg_pathway_download Download one KEGG pathway
kegg_pathway_list List of KEGG pathways
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
kinaseextra Molecular interactions from OmniPath

-- L --

latin_name Latin (scientific) names of organisms
ligrecextra Molecular interactions from OmniPath
lncrna_mrna Molecular interactions from OmniPath
load_config Load the package configuration from a config file
load_db Load a built in database
logfile Path to the current OmnipathR log file

-- M --

metalinksdb_sqlite Open MetalinksDB as an SQLite3 connection
metalinksdb_table A table from MetalinksDB
metalinksdb_tables List tables in MetalinksDB
mirna_target Molecular interactions from OmniPath

-- N --

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

-- O --

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 Molecular interactions from OmniPath
omnipath-interactions Molecular interactions from OmniPath
OmnipathR The OmnipathR package
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 Current config file path of OmnipathR
omnipath_for_cosmos OmniPath PPI for the COSMOS PKN
omnipath_interactions Molecular interactions from OmniPath
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_query Download data from the OmniPath web service
omnipath_reset_config Restore the built-in default values of all config parameters of a package
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
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

-- P --

pathwaycommons_download Interactions from PathwayCommons
pathwayextra Molecular interactions from OmniPath
pivot_annotations Converts annotation tables to a wide format
post_translational Molecular interactions from OmniPath
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

-- Q --

query_info OmniPath query parameters

-- R --

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
read_log Browse the current OmnipathR log file
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
reset_config Restore the built-in default values of all config parameters of a package
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
resource_info OmniPath resource information

-- S --

save_config Save the current package configuration
set_loglevel Sets the log level for the package logger
show_network Visualize node neighborhood with SigmaJS
signed_ptms Causal effect enzyme-PTM interactions
simplify_intercell_network Simplify an intercell network
small_molecule Molecular interactions from OmniPath
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

-- T --

tfcensus_download Downloads the list of transcription factors from TF census
tf_mirna Molecular interactions from OmniPath
tf_target Molecular interactions from OmniPath
transcriptional Molecular interactions from OmniPath
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

-- U --

uniprot_full_id_mapping_table Creates an ID translation table from UniProt data
uniprot_genesymbol_cleanup TrEMBL to SwissProt by gene names
uniprot_idmapping_id_types ID types available in the UniProt ID Mapping service
uniprot_id_mapping_table ID translation data from UniProt ID Mapping
uniprot_id_type UniProt identifier type label
unique_intercell_network Unique intercellular interactions
unnest_evidences Separate evidences by direction and effect sign
uploadlists_id_type UniProt Uploadlists identifier type label

-- V --

vinayagam_download Protein-protein interactions from Vinayagam 2011

-- W --

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

-- Z --

zenodo_download Retrieves data from Zenodo

-- misc --

.omnipathr_options_defaults Default values for the package options