OmnipathR-package	OmnipathR
.omnipathr_options_defaults	dot-omnipathr_options_defaults
all_interactions	omnipath-interactions
all_uniprots	all_uniprots
all_uniprot_acs	all_uniprot_acs
ambiguity	ambiguity
ancestors	ancestors
annotated_network	annotated_network
annotations	annotations
annotation_categories	annotation_categories
annotation_resources	annotation_resources
biomart_query	biomart_query
bioplex1	bioplex1
bioplex2	bioplex2
bioplex3	bioplex3
bioplex_all	bioplex_all
bioplex_hct116_1	bioplex_hct116_1
bma_motif_es	bma_motif_es
bma_motif_vs	bma_motif_vs
chalmers_gem	chalmers_gem
chalmers_gem_id_mapping_table	chalmers_gem_id_mapping_table
chalmers_gem_id_type	chalmers_gem_id_type
chalmers_gem_metabolites	chalmers_gem_metabolites
chalmers_gem_network	chalmers_gem_network
chalmers_gem_raw	chalmers_gem_raw
chalmers_gem_reactions	chalmers_gem_reactions
collectri	omnipath-interactions
common_name	common_name
complexes	complexes
complex_genes	complex_genes
complex_resources	complex_resources
config_path	omnipath_config_path
consensuspathdb_download	consensuspathdb_download
consensuspathdb_raw_table	consensuspathdb_raw_table
cosmos_pkn	cosmos_pkn
curated_ligand_receptor_interactions	curated_ligand_receptor_interactions
curated_ligrec_stats	curated_ligrec_stats
database_summary	database_summary
datasets_one_column	datasets_one_column
descendants	descendants
dorothea	omnipath-interactions
ensembl_dataset	ensembl_dataset
ensembl_id_mapping_table	ensembl_id_mapping_table
ensembl_id_type	ensembl_id_type
ensembl_name	ensembl_name
ensembl_organisms	ensembl_organisms
ensembl_organisms_raw	ensembl_organisms_raw
ensembl_orthology	ensembl_orthology
ensure_igraph	ensure_igraph
enzsub_graph	enzsub_graph
enzsub_resources	enzsub_resources
enzyme_substrate	enzyme_substrate
evex_download	evex_download
evidences	evidences
extra_attrs	extra_attrs
extra_attrs_to_cols	extra_attrs_to_cols
extra_attr_values	extra_attr_values
filter_by_resource	filter_by_resource
filter_evidences	filter_evidences
filter_extra_attrs	filter_extra_attrs
filter_intercell	filter_intercell
filter_intercell_network	filter_intercell_network
find_all_paths	find_all_paths
from_evidences	from_evidences
get_annotation_resources	annotation_resources
get_complex_genes	complex_genes
get_complex_resources	complex_resources
get_db	get_db
get_enzsub_resources	enzsub_resources
get_interaction_resources	interaction_resources
get_intercell_categories	intercell_categories
get_intercell_generic_categories	intercell_generic_categories
get_intercell_resources	intercell_resources
get_ontology_db	get_ontology_db
get_resources	resources
get_signed_ptms	signed_ptms
giant_component	giant_component
go_annot_download	go_annot_download
go_annot_slim	go_annot_slim
go_ontology_download	go_ontology_download
graph_interaction	graph_interaction
guide2pharma_download	guide2pharma_download
harmonizome_download	harmonizome_download
has_extra_attrs	has_extra_attrs
hmdb_id_mapping_table	hmdb_id_mapping_table
hmdb_id_type	hmdb_id_type
hmdb_metabolite_fields	hmdb_metabolite_fields
hmdb_protein_fields	hmdb_protein_fields
hmdb_table	hmdb_table
homologene_download	homologene_download
homologene_organisms	homologene_organisms
homologene_raw	homologene_raw
homologene_uniprot_orthology	homologene_uniprot_orthology
hpo_download	hpo_download
htridb_download	htridb_download
id_translation_resources	id_translation_resources
id_types	id_types
import_all_interactions	omnipath-interactions
import_dorothea_interactions	omnipath-interactions
import_intercell_network	intercell_network
import_kinaseextra_interactions	omnipath-interactions
import_ligrecextra_interactions	omnipath-interactions
import_lncrna_mrna_interactions	omnipath-interactions
import_mirnatarget_interactions	omnipath-interactions
import_omnipath_annotations	annotations
import_omnipath_complexes	complexes
import_omnipath_enzsub	enzyme_substrate
import_omnipath_interactions	omnipath-interactions
import_omnipath_intercell	intercell
import_pathwayextra_interactions	omnipath-interactions
import_post_translational_interactions	omnipath-interactions
import_small_molecule_protein_interactions	omnipath-interactions
import_tf_mirna_interactions	omnipath-interactions
import_tf_target_interactions	omnipath-interactions
import_transcriptional_interactions	omnipath-interactions
inbiomap_download	inbiomap_download
inbiomap_raw	inbiomap_raw
interaction_datasets	interaction_datasets
interaction_graph	interaction_graph
interaction_resources	interaction_resources
interaction_types	interaction_types
intercell	intercell
intercell_categories	intercell_categories
intercell_consensus_filter	intercell_consensus_filter
intercell_generic_categories	intercell_generic_categories
intercell_network	intercell_network
intercell_resources	intercell_resources
intercell_summary	intercell_summary
is_ontology_id	is_ontology_id
is_swissprot	is_swissprot
is_trembl	is_trembl
is_uniprot	is_uniprot
kegg_api_templates	kegg_api_templates
kegg_conv	kegg_conv
kegg_databases	kegg_databases
kegg_ddi	kegg_ddi
kegg_find	kegg_find
kegg_info	kegg_info
kegg_link	kegg_link
kegg_list	kegg_list
kegg_open	kegg_open
kegg_operations	kegg_operations
kegg_organisms	kegg_organisms
kegg_organism_codes	kegg_organism_codes
kegg_pathways_download	kegg_pathways_download
kegg_pathway_annotations	kegg_pathway_annotations
kegg_pathway_download	kegg_pathway_download
kegg_pathway_list	kegg_pathway_list
kegg_picture	kegg_picture
kegg_process	kegg_process
kegg_query	kegg_query
kegg_request	kegg_request
kegg_rm_prefix	kegg_rm_prefix
kinaseextra	omnipath-interactions
latin_name	latin_name
ligrecextra	omnipath-interactions
lncrna_mrna	omnipath-interactions
load_config	omnipath_load_config
load_db	load_db
logfile	omnipath_logfile
metalinksdb_sqlite	metalinksdb_sqlite
metalinksdb_table	metalinksdb_table
metalinksdb_tables	metalinksdb_tables
mirna_target	omnipath-interactions
ncbi_taxid	ncbi_taxid
nichenet_build_model	nichenet_build_model
nichenet_expression_data	nichenet_expression_data
nichenet_gr_network	nichenet_gr_network
nichenet_gr_network_evex	nichenet_gr_network_evex
nichenet_gr_network_harmonizome	nichenet_gr_network_harmonizome
nichenet_gr_network_htridb	nichenet_gr_network_htridb
nichenet_gr_network_omnipath	nichenet_gr_network_omnipath
nichenet_gr_network_pathwaycommons	nichenet_gr_network_pathwaycommons
nichenet_gr_network_regnetwork	nichenet_gr_network_regnetwork
nichenet_gr_network_remap	nichenet_gr_network_remap
nichenet_gr_network_trrust	nichenet_gr_network_trrust
nichenet_ligand_activities	nichenet_ligand_activities
nichenet_ligand_target_links	nichenet_ligand_target_links
nichenet_ligand_target_matrix	nichenet_ligand_target_matrix
nichenet_lr_network	nichenet_lr_network
nichenet_lr_network_guide2pharma	nichenet_lr_network_guide2pharma
nichenet_lr_network_omnipath	nichenet_lr_network_omnipath
nichenet_lr_network_ramilowski	nichenet_lr_network_ramilowski
nichenet_main	nichenet_main
nichenet_networks	nichenet_networks
nichenet_optimization	nichenet_optimization
nichenet_remove_orphan_ligands	nichenet_remove_orphan_ligands
nichenet_results_dir	nichenet_results_dir
nichenet_signaling_network	nichenet_signaling_network
nichenet_signaling_network_cpdb	nichenet_signaling_network_cpdb
nichenet_signaling_network_evex	nichenet_signaling_network_evex
nichenet_signaling_network_harmonizome	nichenet_signaling_network_harmonizome
nichenet_signaling_network_inbiomap	nichenet_signaling_network_inbiomap
nichenet_signaling_network_omnipath	nichenet_signaling_network_omnipath
nichenet_signaling_network_pathwaycommons	nichenet_signaling_network_pathwaycommons
nichenet_signaling_network_vinayagam	nichenet_signaling_network_vinayagam
nichenet_test	nichenet_test
nichenet_workarounds	nichenet_workarounds
obo_parser	obo_parser
oma_code	oma_code
oma_organisms	oma_organisms
oma_pairwise	oma_pairwise
oma_pairwise_genesymbols	oma_pairwise_genesymbols
oma_pairwise_translated	oma_pairwise_translated
omnipath	omnipath-interactions
omnipath-interactions	omnipath-interactions
OmnipathR	OmnipathR
omnipath_cache_autoclean	omnipath_cache_autoclean
omnipath_cache_clean	omnipath_cache_clean
omnipath_cache_clean_db	omnipath_cache_clean_db
omnipath_cache_download_ready	omnipath_cache_download_ready
omnipath_cache_filter_versions	omnipath_cache_filter_versions
omnipath_cache_get	omnipath_cache_get
omnipath_cache_key	omnipath_cache_key
omnipath_cache_latest_or_new	omnipath_cache_latest_or_new
omnipath_cache_latest_version	omnipath_cache_latest_version
omnipath_cache_load	omnipath_cache_load
omnipath_cache_move_in	omnipath_cache_move_in
omnipath_cache_remove	omnipath_cache_remove
omnipath_cache_save	omnipath_cache_save
omnipath_cache_search	omnipath_cache_search
omnipath_cache_set_ext	omnipath_cache_set_ext
omnipath_cache_update_status	omnipath_cache_update_status
omnipath_cache_wipe	omnipath_cache_wipe
omnipath_config_path	omnipath_config_path
omnipath_for_cosmos	omnipath_for_cosmos
omnipath_interactions	omnipath-interactions
omnipath_load_config	omnipath_load_config
omnipath_log	omnipath_log
omnipath_logfile	omnipath_logfile
omnipath_msg	omnipath_msg
omnipath_query	omnipath_query
omnipath_reset_config	omnipath_reset_config
omnipath_save_config	omnipath_save_config
omnipath_set_cachedir	omnipath_set_cachedir
omnipath_set_console_loglevel	omnipath_set_console_loglevel
omnipath_set_logfile_loglevel	omnipath_set_logfile_loglevel
omnipath_set_loglevel	omnipath_set_loglevel
omnipath_show_db	omnipath_show_db
omnipath_unlock_cache_db	omnipath_unlock_cache_db
only_from	only_from
ontology_ensure_id	ontology_ensure_id
ontology_ensure_name	ontology_ensure_name
ontology_name_id	ontology_name_id
organism_for	organism_for
orthology_translate_column	orthology_translate_column
pathwaycommons_download	pathwaycommons_download
pathwayextra	omnipath-interactions
pivot_annotations	pivot_annotations
post_translational	omnipath-interactions
preppi_download	preppi_download
preppi_filter	preppi_filter
print_bma_motif_es	print_bma_motif_es
print_bma_motif_vs	print_bma_motif_vs
print_interactions	print_interactions
print_path_es	print_path_es
print_path_vs	print_path_vs
pubmed_open	pubmed_open
query_info	query_info
ramilowski_download	ramilowski_download
ramp_id_mapping_table	ramp_id_mapping_table
ramp_id_type	ramp_id_type
ramp_sqlite	ramp_sqlite
ramp_table	ramp_table
ramp_tables	ramp_tables
read_log	omnipath_log
regnetwork_directions	regnetwork_directions
regnetwork_download	regnetwork_download
relations_list_to_table	relations_list_to_table
relations_table_to_graph	relations_table_to_graph
relations_table_to_list	relations_table_to_list
remap_dorothea_download	remap_dorothea_download
remap_filtered	remap_filtered
remap_tf_target_download	remap_tf_target_download
reset_config	omnipath_reset_config
resources	resources
resources_colname	resources_colname
resources_in	resources_in
resource_info	resource_info
save_config	omnipath_save_config
set_loglevel	omnipath_set_loglevel
show_network	show_network
signed_ptms	signed_ptms
simplify_intercell_network	simplify_intercell_network
small_molecule	omnipath-interactions
static_table	static_table
static_tables	static_tables
stitch_actions	stitch_actions
stitch_links	stitch_links
stitch_network	stitch_network
stitch_remove_prefixes	stitch_remove_prefixes
subnetwork	subnetwork
swap_relations	swap_relations
swissprots_only	swissprots_only
tfcensus_download	tfcensus_download
tf_mirna	omnipath-interactions
tf_target	omnipath-interactions
transcriptional	omnipath-interactions
translate_ids	translate_ids
translate_ids_multi	translate_ids_multi
trembls_only	trembls_only
trrust_download	trrust_download
uniprot_full_id_mapping_table	uniprot_full_id_mapping_table
uniprot_genesymbol_cleanup	uniprot_genesymbol_cleanup
uniprot_idmapping_id_types	uniprot_idmapping_id_types
uniprot_id_mapping_table	uniprot_id_mapping_table
uniprot_id_type	uniprot_id_type
uniprot_organisms	uniprot_organisms
unique_intercell_network	unique_intercell_network
unnest_evidences	unnest_evidences
uploadlists_id_type	uploadlists_id_type
vinayagam_download	vinayagam_download
walk_ontology_tree	walk_ontology_tree
with_extra_attrs	with_extra_attrs
with_references	with_references
zenodo_download	zenodo_download
