# Generated by roxygen2: do not edit by hand

S3method(group_by,tbl_attrs)
S3method(mutate,tbl_attrs)
S3method(reframe,tbl_attrs)
S3method(rowwise,tbl_attrs)
S3method(summarise,tbl_attrs)
S3method(ungroup,tbl_attrs)
export(all_interactions)
export(all_uniprot_acs)
export(all_uniprots)
export(ambiguity)
export(ancestors)
export(annotated_network)
export(annotation_categories)
export(annotation_resources)
export(annotations)
export(biomart_query)
export(bioplex1)
export(bioplex2)
export(bioplex3)
export(bioplex_all)
export(bioplex_hct116_1)
export(bma_motif_es)
export(bma_motif_vs)
export(chalmers_gem)
export(chalmers_gem_id_mapping_table)
export(chalmers_gem_id_type)
export(chalmers_gem_metabolites)
export(chalmers_gem_network)
export(chalmers_gem_raw)
export(chalmers_gem_reactions)
export(collectri)
export(common_name)
export(complex_genes)
export(complex_resources)
export(complexes)
export(config_path)
export(consensuspathdb_download)
export(consensuspathdb_raw_table)
export(cosmos_pkn)
export(curated_ligand_receptor_interactions)
export(curated_ligrec_stats)
export(database_summary)
export(datasets_one_column)
export(descendants)
export(dorothea)
export(ensembl_dataset)
export(ensembl_id_mapping_table)
export(ensembl_id_type)
export(ensembl_name)
export(ensembl_organisms)
export(ensembl_organisms_raw)
export(ensembl_orthology)
export(ensure_igraph)
export(enzsub_graph)
export(enzsub_resources)
export(enzyme_substrate)
export(evex_download)
export(evidences)
export(extra_attr_values)
export(extra_attrs)
export(extra_attrs_to_cols)
export(filter_by_resource)
export(filter_evidences)
export(filter_extra_attrs)
export(filter_intercell)
export(filter_intercell_network)
export(find_all_paths)
export(from_evidences)
export(get_annotation_resources)
export(get_complex_genes)
export(get_complex_resources)
export(get_db)
export(get_enzsub_resources)
export(get_interaction_resources)
export(get_intercell_categories)
export(get_intercell_generic_categories)
export(get_intercell_resources)
export(get_ontology_db)
export(get_resources)
export(giant_component)
export(go_annot_download)
export(go_annot_slim)
export(go_ontology_download)
export(graph_interaction)
export(guide2pharma_download)
export(harmonizome_download)
export(has_extra_attrs)
export(hmdb_id_mapping_table)
export(hmdb_id_type)
export(hmdb_metabolite_fields)
export(hmdb_protein_fields)
export(hmdb_table)
export(homologene_download)
export(homologene_organisms)
export(homologene_raw)
export(homologene_uniprot_orthology)
export(hpo_download)
export(htridb_download)
export(id_translation_resources)
export(id_types)
export(import_all_interactions)
export(import_dorothea_interactions)
export(import_intercell_network)
export(import_kinaseextra_interactions)
export(import_ligrecextra_interactions)
export(import_lncrna_mrna_interactions)
export(import_mirnatarget_interactions)
export(import_omnipath_annotations)
export(import_omnipath_complexes)
export(import_omnipath_enzsub)
export(import_omnipath_interactions)
export(import_omnipath_intercell)
export(import_pathwayextra_interactions)
export(import_post_translational_interactions)
export(import_small_molecule_protein_interactions)
export(import_tf_mirna_interactions)
export(import_tf_target_interactions)
export(import_transcriptional_interactions)
export(inbiomap_download)
export(inbiomap_raw)
export(interaction_datasets)
export(interaction_graph)
export(interaction_resources)
export(interaction_types)
export(intercell)
export(intercell_categories)
export(intercell_consensus_filter)
export(intercell_generic_categories)
export(intercell_network)
export(intercell_resources)
export(intercell_summary)
export(is_ontology_id)
export(is_swissprot)
export(is_trembl)
export(is_uniprot)
export(kegg_api_templates)
export(kegg_conv)
export(kegg_databases)
export(kegg_ddi)
export(kegg_find)
export(kegg_info)
export(kegg_link)
export(kegg_list)
export(kegg_open)
export(kegg_operations)
export(kegg_organism_codes)
export(kegg_organisms)
export(kegg_pathway_annotations)
export(kegg_pathway_download)
export(kegg_pathway_list)
export(kegg_pathways_download)
export(kegg_picture)
export(kegg_process)
export(kegg_query)
export(kegg_request)
export(kegg_rm_prefix)
export(kinaseextra)
export(latin_name)
export(ligrecextra)
export(lncrna_mrna)
export(load_config)
export(load_db)
export(logfile)
export(metalinksdb_sqlite)
export(metalinksdb_table)
export(metalinksdb_tables)
export(mirna_target)
export(ncbi_taxid)
export(nichenet_build_model)
export(nichenet_expression_data)
export(nichenet_gr_network)
export(nichenet_gr_network_evex)
export(nichenet_gr_network_harmonizome)
export(nichenet_gr_network_htridb)
export(nichenet_gr_network_omnipath)
export(nichenet_gr_network_pathwaycommons)
export(nichenet_gr_network_regnetwork)
export(nichenet_gr_network_remap)
export(nichenet_gr_network_trrust)
export(nichenet_ligand_activities)
export(nichenet_ligand_target_links)
export(nichenet_ligand_target_matrix)
export(nichenet_lr_network)
export(nichenet_lr_network_guide2pharma)
export(nichenet_lr_network_omnipath)
export(nichenet_lr_network_ramilowski)
export(nichenet_main)
export(nichenet_networks)
export(nichenet_optimization)
export(nichenet_remove_orphan_ligands)
export(nichenet_results_dir)
export(nichenet_signaling_network)
export(nichenet_signaling_network_cpdb)
export(nichenet_signaling_network_evex)
export(nichenet_signaling_network_harmonizome)
export(nichenet_signaling_network_inbiomap)
export(nichenet_signaling_network_omnipath)
export(nichenet_signaling_network_pathwaycommons)
export(nichenet_signaling_network_vinayagam)
export(nichenet_test)
export(nichenet_workarounds)
export(obo_parser)
export(oma_code)
export(oma_organisms)
export(oma_pairwise)
export(oma_pairwise_genesymbols)
export(oma_pairwise_translated)
export(omnipath)
export(omnipath_cache_autoclean)
export(omnipath_cache_clean)
export(omnipath_cache_clean_db)
export(omnipath_cache_download_ready)
export(omnipath_cache_filter_versions)
export(omnipath_cache_get)
export(omnipath_cache_key)
export(omnipath_cache_latest_or_new)
export(omnipath_cache_latest_version)
export(omnipath_cache_load)
export(omnipath_cache_move_in)
export(omnipath_cache_remove)
export(omnipath_cache_save)
export(omnipath_cache_search)
export(omnipath_cache_set_ext)
export(omnipath_cache_update_status)
export(omnipath_cache_wipe)
export(omnipath_config_path)
export(omnipath_for_cosmos)
export(omnipath_interactions)
export(omnipath_load_config)
export(omnipath_log)
export(omnipath_logfile)
export(omnipath_msg)
export(omnipath_query)
export(omnipath_reset_config)
export(omnipath_save_config)
export(omnipath_set_cachedir)
export(omnipath_set_console_loglevel)
export(omnipath_set_logfile_loglevel)
export(omnipath_set_loglevel)
export(omnipath_show_db)
export(omnipath_unlock_cache_db)
export(only_from)
export(ontology_ensure_id)
export(ontology_ensure_name)
export(ontology_name_id)
export(organism_for)
export(orthology_translate_column)
export(pathwaycommons_download)
export(pathwayextra)
export(pivot_annotations)
export(post_translational)
export(preppi_download)
export(preppi_filter)
export(print_bma_motif_es)
export(print_bma_motif_vs)
export(print_interactions)
export(print_path_es)
export(print_path_vs)
export(pubmed_open)
export(query_info)
export(ramilowski_download)
export(ramp_id_mapping_table)
export(ramp_id_type)
export(ramp_sqlite)
export(ramp_table)
export(ramp_tables)
export(read_log)
export(regnetwork_directions)
export(regnetwork_download)
export(relations_list_to_table)
export(relations_table_to_graph)
export(relations_table_to_list)
export(remap_dorothea_download)
export(remap_filtered)
export(remap_tf_target_download)
export(reset_config)
export(resource_info)
export(resources)
export(resources_colname)
export(resources_in)
export(save_config)
export(set_loglevel)
export(show_network)
export(signed_ptms)
export(simplify_intercell_network)
export(small_molecule)
export(static_table)
export(static_tables)
export(stitch_actions)
export(stitch_links)
export(stitch_network)
export(stitch_remove_prefixes)
export(subnetwork)
export(swap_relations)
export(swissprots_only)
export(tf_mirna)
export(tf_target)
export(tfcensus_download)
export(transcriptional)
export(translate_ids)
export(translate_ids_multi)
export(trembls_only)
export(trrust_download)
export(uniprot_full_id_mapping_table)
export(uniprot_genesymbol_cleanup)
export(uniprot_id_mapping_table)
export(uniprot_id_type)
export(uniprot_idmapping_id_types)
export(uniprot_organisms)
export(unique_intercell_network)
export(unnest_evidences)
export(uploadlists_id_type)
export(vinayagam_download)
export(walk_ontology_tree)
export(with_extra_attrs)
export(with_references)
export(zenodo_download)
import(logger)
importFrom(R.utils,decompressFile)
importFrom(RSQLite,SQLite)
importFrom(RSQLite,dbConnect)
importFrom(RSQLite,dbDisconnect)
importFrom(RSQLite,dbListTables)
importFrom(RSQLite,dbReadTable)
importFrom(XML,xmlEventParse)
importFrom(checkmate,assert_data_frame)
importFrom(crayon,num_colors)
importFrom(curl,curl)
importFrom(curl,curl_fetch_disk)
importFrom(curl,curl_fetch_memory)
importFrom(curl,curl_options)
importFrom(curl,curl_version)
importFrom(curl,handle_cookies)
importFrom(curl,handle_data)
importFrom(curl,handle_setopt)
importFrom(curl,new_handle)
importFrom(digest,sha1_digest)
importFrom(dplyr,across)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_cols)
importFrom(dplyr,bind_rows)
importFrom(dplyr,c_across)
importFrom(dplyr,case_when)
importFrom(dplyr,coalesce)
importFrom(dplyr,cur_group_id)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,first)
importFrom(dplyr,full_join)
importFrom(dplyr,group_by)
importFrom(dplyr,group_keys)
importFrom(dplyr,group_split)
importFrom(dplyr,if_any)
importFrom(dplyr,inner_join)
importFrom(dplyr,join_by)
importFrom(dplyr,last)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,mutate_all)
importFrom(dplyr,n)
importFrom(dplyr,n_distinct)
importFrom(dplyr,na_if)
importFrom(dplyr,pick)
importFrom(dplyr,pull)
importFrom(dplyr,recode)
importFrom(dplyr,reframe)
importFrom(dplyr,relocate)
importFrom(dplyr,rename)
importFrom(dplyr,rename_all)
importFrom(dplyr,rename_with)
importFrom(dplyr,row_number)
importFrom(dplyr,rowwise)
importFrom(dplyr,sample_frac)
importFrom(dplyr,select)
importFrom(dplyr,slice)
importFrom(dplyr,slice_head)
importFrom(dplyr,slice_max)
importFrom(dplyr,slice_tail)
importFrom(dplyr,summarise)
importFrom(dplyr,summarise_at)
importFrom(dplyr,summarize)
importFrom(dplyr,summarize_all)
importFrom(dplyr,ungroup)
importFrom(fs,path_ext)
importFrom(httr2,req_body_form)
importFrom(httr2,req_body_json)
importFrom(httr2,req_body_raw)
importFrom(httr2,req_headers)
importFrom(httr2,req_options)
importFrom(httr2,req_perform)
importFrom(httr2,request)
importFrom(httr2,resp_body_json)
importFrom(httr2,resp_body_string)
importFrom(httr2,resp_headers)
importFrom(httr2,resp_status)
importFrom(httr2,resp_status_desc)
importFrom(httr2,url_parse)
importFrom(igraph,"%->%")
importFrom(igraph,"E<-")
importFrom(igraph,"V<-")
importFrom(igraph,E)
importFrom(igraph,V)
importFrom(igraph,as.directed)
importFrom(igraph,as_data_frame)
importFrom(igraph,components)
importFrom(igraph,degree)
importFrom(igraph,delete_edges)
importFrom(igraph,ecount)
importFrom(igraph,ego)
importFrom(igraph,get.edgelist)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,graph_from_literal)
importFrom(igraph,head_of)
importFrom(igraph,induced_subgraph)
importFrom(igraph,is_igraph)
importFrom(igraph,neighborhood)
importFrom(igraph,shortest_paths)
importFrom(igraph,tail_of)
importFrom(igraph,vcount)
importFrom(igraph,vertex_attr)
importFrom(igraph,vertex_attr_names)
importFrom(jsonlite,fromJSON)
importFrom(jsonlite,toJSON)
importFrom(jsonlite,validate)
importFrom(later,create_loop)
importFrom(later,destroy_loop)
importFrom(later,global_loop)
importFrom(later,later)
importFrom(logger,appender_console)
importFrom(logger,appender_file)
importFrom(logger,formatter_glue_or_sprintf)
importFrom(logger,layout_glue_generator)
importFrom(logger,log_appender)
importFrom(logger,log_error)
importFrom(logger,log_fatal)
importFrom(logger,log_formatter)
importFrom(logger,log_info)
importFrom(logger,log_layout)
importFrom(logger,log_level)
importFrom(logger,log_success)
importFrom(logger,log_threshold)
importFrom(logger,log_trace)
importFrom(logger,log_warn)
importFrom(lubridate,dmy)
importFrom(lubridate,hm)
importFrom(lubridate,seconds_to_period)
importFrom(magrittr,"%<>%")
importFrom(magrittr,"%>%")
importFrom(magrittr,"%T>%")
importFrom(magrittr,add)
importFrom(magrittr,and)
importFrom(magrittr,equals)
importFrom(magrittr,extract)
importFrom(magrittr,extract2)
importFrom(magrittr,inset)
importFrom(magrittr,inset2)
importFrom(magrittr,is_greater_than)
importFrom(magrittr,is_in)
importFrom(magrittr,is_less_than)
importFrom(magrittr,not)
importFrom(magrittr,or)
importFrom(magrittr,set_attr)
importFrom(magrittr,set_colnames)
importFrom(magrittr,subtract)
importFrom(progress,progress_bar)
importFrom(purrr,compose)
importFrom(purrr,cross2)
importFrom(purrr,detect)
importFrom(purrr,discard)
importFrom(purrr,keep)
importFrom(purrr,map)
importFrom(purrr,map2)
importFrom(purrr,map2_chr)
importFrom(purrr,map_chr)
importFrom(purrr,map_dbl)
importFrom(purrr,map_int)
importFrom(purrr,map_lgl)
importFrom(purrr,partial)
importFrom(purrr,pluck)
importFrom(purrr,pmap)
importFrom(purrr,pmap_chr)
importFrom(purrr,pmap_int)
importFrom(purrr,pmap_lgl)
importFrom(purrr,reduce)
importFrom(purrr,reduce2)
importFrom(purrr,safely)
importFrom(purrr,transpose)
importFrom(purrr,walk)
importFrom(purrr,walk2)
importFrom(rappdirs,user_cache_dir)
importFrom(rappdirs,user_config_dir)
importFrom(readr,col_character)
importFrom(readr,col_date)
importFrom(readr,col_factor)
importFrom(readr,col_integer)
importFrom(readr,col_number)
importFrom(readr,col_skip)
importFrom(readr,cols)
importFrom(readr,read_delim)
importFrom(readr,read_file)
importFrom(readr,read_lines)
importFrom(readr,read_tsv)
importFrom(readr,type_convert)
importFrom(readr,with_edition)
importFrom(readxl,read_excel)
importFrom(rlang,"!!!")
importFrom(rlang,"!!")
importFrom(rlang,"%||%")
importFrom(rlang,":=")
importFrom(rlang,.data)
importFrom(rlang,are_na)
importFrom(rlang,as_function)
importFrom(rlang,enexprs)
importFrom(rlang,enquo)
importFrom(rlang,enquos)
importFrom(rlang,ensyms)
importFrom(rlang,eval_tidy)
importFrom(rlang,exec)
importFrom(rlang,expr)
importFrom(rlang,exprs)
importFrom(rlang,fn_fmls_names)
importFrom(rlang,is_function)
importFrom(rlang,is_integer)
importFrom(rlang,is_list)
importFrom(rlang,is_symbol)
importFrom(rlang,list2)
importFrom(rlang,parse_expr)
importFrom(rlang,quo_get_expr)
importFrom(rlang,quo_text)
importFrom(rlang,set_names)
importFrom(rlang,sym)
importFrom(rlang,syms)
importFrom(rlang,wref_key)
importFrom(rmarkdown,pandoc_version)
importFrom(rvest,html_element)
importFrom(rvest,html_table)
importFrom(rvest,read_html)
importFrom(sessioninfo,session_info)
importFrom(stats,na.omit)
importFrom(stats,quantile)
importFrom(stringi,stri_locate_all_fixed)
importFrom(stringi,stri_locate_first_fixed)
importFrom(stringi,stri_locate_last_fixed)
importFrom(stringi,stri_split_lines1)
importFrom(stringr,str_c)
importFrom(stringr,str_count)
importFrom(stringr,str_detect)
importFrom(stringr,str_extract)
importFrom(stringr,str_extract_all)
importFrom(stringr,str_match)
importFrom(stringr,str_pad)
importFrom(stringr,str_remove)
importFrom(stringr,str_replace)
importFrom(stringr,str_replace_all)
importFrom(stringr,str_split)
importFrom(stringr,str_split_fixed)
importFrom(stringr,str_starts)
importFrom(stringr,str_sub)
importFrom(stringr,str_to_lower)
importFrom(stringr,str_to_upper)
importFrom(stringr,str_trim)
importFrom(stringr,str_trunc)
importFrom(tibble,as_tibble)
importFrom(tibble,rownames_to_column)
importFrom(tibble,tibble)
importFrom(tidyr,chop)
importFrom(tidyr,expand_grid)
importFrom(tidyr,nest)
importFrom(tidyr,pivot_wider)
importFrom(tidyr,replace_na)
importFrom(tidyr,separate)
importFrom(tidyr,separate_longer_delim)
importFrom(tidyr,separate_rows)
importFrom(tidyr,separate_wider_delim)
importFrom(tidyr,separate_wider_regex)
importFrom(tidyr,unite)
importFrom(tidyr,unnest)
importFrom(tidyr,unnest_longer)
importFrom(tidyr,unnest_wider)
importFrom(tidyselect,all_of)
importFrom(tidyselect,any_of)
importFrom(tidyselect,ends_with)
importFrom(tidyselect,eval_select)
importFrom(tidyselect,everything)
importFrom(tidyselect,last_col)
importFrom(tidyselect,starts_with)
importFrom(tidyselect,vars_select_helpers)
importFrom(tidyselect,where)
importFrom(tools,file_path_sans_ext)
importFrom(utils,URLencode)
importFrom(utils,browseURL)
importFrom(utils,capture.output)
importFrom(utils,flush.console)
importFrom(utils,head)
importFrom(utils,installed.packages)
importFrom(utils,modifyList)
importFrom(utils,object.size)
importFrom(utils,packageDescription)
importFrom(utils,packageName)
importFrom(utils,packageVersion)
importFrom(utils,tail)
importFrom(utils,untar)
importFrom(utils,unzip)
importFrom(vctrs,vec_cast)
importFrom(withr,local_options)
importFrom(xml2,read_html)
importFrom(xml2,read_xml)
importFrom(xml2,xml_attr)
importFrom(xml2,xml_child)
importFrom(xml2,xml_children)
importFrom(xml2,xml_find_all)
importFrom(xml2,xml_find_first)
importFrom(xml2,xml_ns)
importFrom(xml2,xml_text)
importFrom(yaml,read_yaml)
importFrom(yaml,write_yaml)
importFrom(zip,zip_list)
