API for saezlab/OmnipathR
OmniPath web service client and more

Global functions
.load_organisms	Source code
.nse_ensure_str	Source code
.omnipathr_options_defaults	Man page
.onLoad	Source code
OmnipathR	Man page
OmnipathR-package	Man page
all_interactions	Man page
all_uniprot_acs	Man page Source code
all_uniprots	Man page Source code
ancestors	Man page
annotated_network	Man page Source code
annotation_categories	Man page
annotation_resources	Man page
annotations	Man page Source code
annotations_search_index	Source code
biomart_query	Man page Source code
bioplex1	Man page Source code
bioplex2	Man page Source code
bioplex3	Man page Source code
bioplex_all	Man page Source code
bioplex_download	Source code
bioplex_hct116_1	Man page Source code
bma_description	Source code
bma_formula	Source code
bma_motif_es	Man page Source code
bma_motif_vs	Man page Source code
bma_relationship	Source code
bma_variable_layout	Source code
bma_variable_model	Source code
build_index	Source code
build_index_impl	Source code
chalmers_gem	Man page Source code
chalmers_gem_id_mapping_table	Man page
chalmers_gem_id_type	Man page
chalmers_gem_metabolites	Man page
chalmers_gem_network	Man page
chalmers_gem_raw	Man page
chalmers_gem_reactions	Man page
collectri	Man page
common_name	Man page Source code
complex_genes	Man page Source code
complex_resources	Man page Source code
complexes	Man page Source code
complexes_search_index	Source code
config_path	Man page
consensuspathdb_download	Man page Source code
consensuspathdb_raw_table	Man page Source code
console_loglevel	Source code
cookie	Man page Source code
cosmos_pkn	Man page Source code
curated_ligand_receptor_interactions	Man page Source code
curated_ligrec_stats	Man page
database_summary	Man page
datasets_one_column	Man page
default_options	Source code
descendants	Man page
deserialize_evidences	Source code
deserialize_extra_attrs	Source code
deserialize_json_col	Source code
dorothea	Man page
empty_char_tibble	Source code
ensembl_dataset	Man page
ensembl_id_mapping_table	Man page
ensembl_id_type	Man page
ensembl_name	Man page Source code
ensembl_organisms	Man page Source code
ensembl_organisms_raw	Man page Source code
ensembl_orthology	Man page
ensure_entity_type	Source code
ensure_igraph	Man page
ensure_loglevel	Source code
enzsub_graph	Man page Source code
enzsub_resources	Man page Source code
enzsub_search_index	Source code
enzyme_substrate	Man page Source code
evex_download	Man page Source code
evidences	Man page
extra_attr_values	Man page
extra_attrs	Man page
extra_attrs_to_cols	Man page
filter_by_resource	Man page Source code
filter_evidences	Man page
filter_extra_attrs	Man page
filter_intercell	Man page
filter_intercell_network	Man page
find_all_paths	Man page Source code
format_graph_edges	Source code
from_evidences	Man page
get_annotation_resources	Man page
get_complex_genes	Man page Source code
get_complex_resources	Man page Source code
get_db	Man page
get_enzsub_resources	Man page Source code
get_index	Source code
get_interaction_resources	Man page
get_intercell_categories	Man page
get_intercell_generic_categories	Man page
get_intercell_resources	Man page
get_ontology_db	Man page
get_resources	Man page Source code
get_signed_ptms	Man page
giant_component	Man page
go_annot_download	Man page Source code
go_annot_slim	Man page Source code
go_ontology_download	Man page Source code
graph_interaction	Man page
guide2pharma_download	Man page Source code
harmonizome_download	Man page Source code
has_evidences	Source code
has_evidences_wide	Source code
has_extra_attrs	Man page
hmdb_id_mapping_table	Man page
hmdb_id_type	Man page
hmdb_metabolite_fields	Man page Source code
hmdb_protein_fields	Man page Source code
hmdb_table	Man page
hmdb_xml2_parse	Source code
homologene_download	Man page Source code
homologene_organisms	Man page Source code
homologene_raw	Man page Source code
homologene_uniprot_orthology	Man page Source code
homology_translate	Source code
hpo_download	Man page Source code
htridb_download	Man page Source code
id_translation_resources	Man page
id_types	Man page
import_all_interactions	Man page
import_dorothea_interactions	Man page
import_intercell_network	Man page
import_kinaseextra_interactions	Man page
import_ligrecextra_interactions	Man page
import_lncrna_mrna_interactions	Man page
import_mirnatarget_interactions	Man page
import_omnipath_annotations	Man page
import_omnipath_complexes	Man page Source code
import_omnipath_enzsub	Man page Source code
import_omnipath_interactions	Man page
import_omnipath_intercell	Man page Source code
import_pathwayextra_interactions	Man page
import_post_translational_interactions	Man page
import_small_molecule_protein_interactions	Man page
import_tf_mirna_interactions	Man page
import_tf_target_interactions	Man page
import_transcriptional_interactions	Man page
inbiomap_download	Man page Source code
inbiomap_raw	Man page Source code
interaction_datasets	Man page
interaction_graph	Man page Source code
interaction_resources	Man page
interaction_types	Man page
interactions_search_index	Source code
intercell	Man page Source code
intercell_categories	Man page
intercell_consensus_filter	Man page Source code
intercell_generic_categories	Man page
intercell_network	Man page
intercell_resources	Man page
intercell_search_index	Source code
intercell_summary	Man page
is_ontology_id	Man page
is_swissprot	Man page
is_trembl	Man page
is_uniprot	Man page
kegg_info	Man page
kegg_open	Man page
kegg_pathway_annotations	Man page
kegg_pathway_download	Man page
kegg_pathway_list	Man page Source code
kegg_pathways_download	Man page Source code
kegg_picture	Man page
kegg_process	Man page
kinaseextra	Man page
latin_name	Man page Source code
ligrecextra	Man page
lncrna_mrna	Man page
load_config	Man page
load_db	Man page
logfile	Man page Source code
mirna_or_protein	Source code
mirna_target	Man page
must_have_evidences	Source code
ncbi_taxid	Man page Source code
nichenet_build_model	Man page
nichenet_expression_data	Man page
nichenet_gr_network	Man page
nichenet_gr_network_evex	Man page
nichenet_gr_network_harmonizome	Man page
nichenet_gr_network_htridb	Man page
nichenet_gr_network_omnipath	Man page
nichenet_gr_network_pathwaycommons	Man page
nichenet_gr_network_regnetwork	Man page
nichenet_gr_network_remap	Man page
nichenet_gr_network_trrust	Man page
nichenet_ligand_activities	Man page
nichenet_ligand_target_links	Man page
nichenet_ligand_target_matrix	Man page
nichenet_lr_network	Man page
nichenet_lr_network_guide2pharma	Man page
nichenet_lr_network_omnipath	Man page
nichenet_lr_network_ramilowski	Man page
nichenet_main	Man page Source code
nichenet_networks	Man page
nichenet_optimization	Man page
nichenet_remove_orphan_ligands	Man page
nichenet_results_dir	Man page
nichenet_signaling_network	Man page
nichenet_signaling_network_cpdb	Man page
nichenet_signaling_network_evex	Man page
nichenet_signaling_network_harmonizome	Man page
nichenet_signaling_network_inbiomap	Man page
nichenet_signaling_network_omnipath	Man page
nichenet_signaling_network_pathwaycommons	Man page
nichenet_signaling_network_vinayagam	Man page
nichenet_test	Man page
nichenet_workarounds	Man page
no_colorout	Source code
nse_test	Source code
obo_parser	Man page Source code
oma_code	Man page Source code
oma_organisms	Man page Source code
oma_pairwise	Man page Source code
oma_pairwise_genesymbols	Man page
oma_pairwise_translated	Man page
oma_supported_organisms	Source code
omnipath	Man page
omnipath-interactions	Man page
omnipath_cache_autoclean	Man page
omnipath_cache_clean	Man page
omnipath_cache_clean_db	Man page
omnipath_cache_download_ready	Man page
omnipath_cache_filter_versions	Man page
omnipath_cache_get	Man page
omnipath_cache_key	Man page
omnipath_cache_latest_or_new	Man page
omnipath_cache_latest_version	Man page
omnipath_cache_load	Man page
omnipath_cache_move_in	Man page
omnipath_cache_remove	Man page
omnipath_cache_save	Man page
omnipath_cache_search	Man page
omnipath_cache_set_ext	Man page
omnipath_cache_update_status	Man page
omnipath_cache_wipe	Man page
omnipath_config_path	Man page
omnipath_console_loglevel	Source code
omnipath_default_cachedir	Source code
omnipath_for_cosmos	Man page
omnipath_get_cachedir	Source code
omnipath_init_cache	Source code
omnipath_init_db	Source code
omnipath_interactions	Man page Source code
omnipath_is_cachedir	Source code
omnipath_load_config	Man page
omnipath_lock_cache_db	Source code
omnipath_log	Man page Source code
omnipath_logfile	Man page Source code
omnipath_msg	Man page Source code
omnipath_new_cachedir	Source code
omnipath_query	Man page Source code
omnipath_reset_config	Man page
omnipath_save_config	Man page
omnipath_set_cachedir	Man page Source code
omnipath_set_console_loglevel	Man page Source code
omnipath_set_logfile_loglevel	Man page Source code
omnipath_set_loglevel	Man page Source code
omnipath_show_db	Man page Source code
omnipath_unlock_cache_db	Man page Source code
omnipath_url	Source code
only_from	Man page
ontology_ensure_id	Man page
ontology_ensure_name	Man page
ontology_name_id	Man page
organism_for	Man page Source code
orthology_translate	Source code
orthology_translate_column	Man page
parse_in_chunks	Source code
patch_logger_appender	Source code
pathwaycommons_download	Man page Source code
pathwayextra	Man page
pivot_annotations	Man page
post_payload	Source code
post_translational	Man page
preppi_download	Man page Source code
preppi_filter	Man page Source code
print_bma_motif_es	Man page Source code
print_bma_motif_vs	Man page
print_interactions	Man page Source code
print_path_es	Man page Source code
print_path_vs	Man page Source code
pubmed_open	Man page Source code
query_info	Man page Source code
ramilowski_download	Man page Source code
ramp_id_mapping_table	Man page
ramp_id_type	Man page
ramp_sqlite	Man page Source code
ramp_table	Man page
ramp_tables	Man page
read_log	Man page Source code
regnetwork_directions	Man page Source code
regnetwork_download	Man page Source code
regnetwork_error	Source code
relations_list_to_table	Man page Source code
relations_table_to_graph	Man page
relations_table_to_list	Man page Source code
remap_dorothea_download	Man page Source code
remap_filtered	Man page Source code
remap_tf_target_download	Man page Source code
remove_tasks	Source code
reset_config	Man page
resource_info	Man page Source code
resources	Man page Source code
resources_colname	Man page Source code
resources_in	Man page
save_config	Man page
search_omnipath	Source code
set_loglevel	Man page Source code
show_network	Man page Source code
signed_ptms	Man page Source code
simplify_intercell_network	Man page
small_molecule	Man page
static_table	Man page
static_tables	Man page Source code
stitch_actions	Man page Source code
stitch_links	Man page Source code
stitch_network	Man page Source code
stitch_remove_prefixes	Man page Source code
strip_resource_labels	Source code
subnetwork	Man page
swap_relations	Man page
swissprots_only	Man page
taxon_name	Source code
taxon_names_table	Source code
tf_mirna	Man page
tf_target	Man page
tfcensus_download	Man page Source code
transcriptional	Man page
translate_ids	Man page
translate_ids_multi	Man page
trembls_only	Man page
trrust_download	Man page Source code
uniprot_full_id_mapping_table	Man page
uniprot_genesymbol_cleanup	Man page
uniprot_id_mapping_table	Man page Source code
uniprot_id_type	Man page
uniprot_idmapping_id_types	Man page
unique_intercell_network	Man page
unique_node_seq	Source code
unnest_evidences	Man page Source code
uploadlists_id_type	Man page
vinayagam_download	Man page Source code
walk_ontology_tree	Man page
with_extra_attrs	Man page
with_references	Man page
wrong_input	Source code
zenodo_download	Man page Source code