saezlab/OmnipathR
OmniPath web service client and more

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455
Source code
63
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233
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saezlab/OmnipathR: OmniPath web service client and more
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API

API for saezlab/OmnipathR
OmniPath web service client and more

Global functions
.nse_ensure_str Source code
.omnipath_options_defaults Man page
.onLoad Source code
.with_references Source code
OmnipathR Man page
OmnipathR-package 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 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
collectri Man page Source code
common_name Man page Source code
complexes_search_index Source code
consensuspathdb_download Man page Source code
consensuspathdb_raw_table Man page Source code
cookie 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 Source code
descendants Man page
deserialize_evidences Source code
deserialize_extra_attrs Source code
deserialize_json_col Source code
dorothea Man page Source code
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_igraph Man page
ensure_loglevel Source code
enzsub_graph Man page Source code
enzsub_search_index 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
filter_sources Man page Source code
find_all_paths Man page Source code
format_graph_edges Source code
from_evidences Man page
get_annotation_databases Man page Source code
get_annotation_resources Man page Source code
get_complex_genes Man page Source code
get_complex_resources Man page Source code
get_complexes_databases Man page Source code
get_db Man page
get_enzsub_resources Man page Source code
get_index Source code
get_interaction_databases Man page Source code
get_interaction_resources Man page Source code
get_intercell_categories Man page
get_intercell_classes Man page
get_intercell_generic_categories Man page
get_intercell_resources Man page
get_ontology_db Man page
get_ptms_databases Man page Source code
get_resources Man page Source code
get_signed_ptms Man page Source code
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
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
import_AllInteractions Man page Source code
import_KinaseExtra_Interactions Man page Source code
import_LigrecExtra_Interactions Man page Source code
import_OmniPath_Interactions Man page Source code
import_OmniPath_PTMS Man page Source code
import_OmniPath_annotations Man page Source code
import_OmniPath_complexes Man page Source code
import_OmniPath_intercell Man page
import_Omnipath_Interactions Man page Source code
import_Omnipath_PTMS Man page Source code
import_Omnipath_annotations Man page Source code
import_Omnipath_complexes Man page Source code
import_Omnipath_intercell Man page
import_PathwayExtra_Interactions Man page Source code
import_all_interactions Man page Source code
import_dorothea_interactions Man page Source code
import_intercell_network Man page
import_kinaseextra_interactions Man page Source code
import_ligrecextra_interactions Man page Source code
import_lncrna_mrna_interactions Man page Source code
import_miRNAtarget_Interactions Man page Source code
import_mirnatarget_interactions Man page Source code
import_omnipath Source code
import_omnipath_annotations Man page Source code
import_omnipath_complexes Man page Source code
import_omnipath_enzsub Man page Source code
import_omnipath_interactions Man page Source code
import_omnipath_intercell Man page Source code
import_pathwayextra_interactions Man page Source code
import_post_translational_interactions Man page Source code
import_small_molecule_protein_interactions Man page Source code
import_tf_mirna_interactions Man page Source code
import_tf_target_interactions Man page Source code
import_tfregulons_interactions Man page Source code
import_transcriptional_interactions Man page Source code
inbiomap_download Man page Source code
inbiomap_raw Man page Source code
interaction_datasets Man page Source code
interaction_graph Man page Source code
interaction_types Man page Source code
interactions_search_index Source code
intercell_categories Man page
intercell_consensus_filter Man page Source code
intercell_search_index Source code
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
latin_name Man page Source code
load_db Man page
mirna_or_protein Source code
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
omnipath Man page Source code
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_console_loglevel Source code
omnipath_default_cachedir Source code
omnipath_get_cachedir Source code
omnipath_get_config_path Man page Source code
omnipath_get_default_config_path Source code
omnipath_get_user_config_path Source code
omnipath_init_cache Source code
omnipath_init_db Source code
omnipath_is_cachedir Source code
omnipath_load_config Man page Source code
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_reset_config Man page
omnipath_save_config Man page Source code
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
orthology_translate Source code
orthology_translate_column Man page
patch_logger_appender Source code
pathwaycommons_download Man page Source code
pivot_annotations Man page Source code
post_payload Source code
preppi_download Man page Source code
preppi_filter Man page Source code
printPath_es Man page Source code
printPath_vs 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
ptms_graph Man page Source code
pubmed_open Man page Source code
query_info Man page Source code
ramilowski_download 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
resource_info Man page Source code
resources_colname Man page Source code
resources_in Man page
search_omnipath Source code
select_interaction_datasets Source code
show_network Man page Source code
simplify_intercell_network Man page
static_table Man page
static_tables 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
tfcensus_download Man page Source code
translate_ids 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 Source code
wrong_input Source code
zenodo_download Man page Source code
saezlab/OmnipathR documentation built on April 17, 2024, 9:39 p.m.

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