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 |
annotation_resources | Retrieves a list of available resources in the annotations... |
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,... |
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... |
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 |
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 |
consensuspathdb_download | Retrieves the ConsensusPathDB network |
consensuspathdb_raw_table | Downloads interaction data from ConsensusPathDB |
cookie | Acquire a cookie if necessary |
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... |
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 |
dot-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... |
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 |
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... |
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... |
intercell_network | Intercellular communication network |
intercell_resources | Retrieves a list of intercellular communication resources... |
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_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... |
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... |
omnipath_cache_autoclean | Keeps only the latest versions of complete downloads |
omnipath_cache_clean | Removes the items from the cache directory which are unknown... |
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... |
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 |
OmnipathR | The OmnipathR package |
omnipath_reset_config | Restore 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 |
only_from | Recreate interaction data frame based on certain datasets and... |
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... |
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.... |
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... |
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_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 |
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 |
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