Collects the names of the resources available in OmniPath for a certain query type and optionally for a dataset within that.
Arguments
- query_type
one of the query types `interactions`, `enz_sub`, `complexes`, `annotations` or `intercell`
- datasets
currently within the `interactions` query type only, multiple datasets are available: `omnipath`, `kinaseextra`, `pathwayextra`, `ligrecextra`, `dorothea`, `tf_target`, `tf_mirna`, `mirnatarget` and `lncrna_mrna`.
- generic_categories
for the `intercell` query type, restrict the search for some generic categories e.g. `ligand` or `receptor`.
Examples
get_resources(query_type = 'interactions')
#> [1] "ABS" "ACSN"
#> [3] "ACSN_SignaLink3" "ARACNe-GTEx_DoRothEA"
#> [5] "ARN" "Adhesome"
#> [7] "AlzPathway" "BEL-Large-Corpus_ProtMapper"
#> [9] "Baccin2019" "BioGRID"
#> [11] "CA1" "CancerCellMap"
#> [13] "CancerDrugsDB" "CellCall"
#> [15] "CellChatDB" "CellChatDB-cofactors"
#> [17] "CellPhoneDB" "CellPhoneDB_Cellinker"
#> [19] "CellTalkDB" "Cellinker"
#> [21] "CollecTRI" "Cui2007"
#> [23] "CytReg_CollecTRI" "DEPOD"
#> [25] "DIP" "DLRP_Cellinker"
#> [27] "DLRP_talklr" "DOMINO"
#> [29] "DeathDomain" "DoRothEA"
#> [31] "DoRothEA-A_CollecTRI" "DoRothEA-reviews_DoRothEA"
#> [33] "ELM" "EMBRACE"
#> [35] "ENCODE-distal" "ENCODE-proximal"
#> [37] "ENCODE_tf-mirna" "ExTRI_CollecTRI"
#> [39] "FANTOM4_DoRothEA" "Fantom5_LRdb"
#> [41] "GEREDB_CollecTRI" "GOA_CollecTRI"
#> [43] "Guide2Pharma" "Guide2Pharma_Cellinker"
#> [45] "Guide2Pharma_LRdb" "Guide2Pharma_talklr"
#> [47] "HOCOMOCO_DoRothEA" "HPMR"
#> [49] "HPMR_Cellinker" "HPMR_LRdb"
#> [51] "HPMR_talklr" "HPRD"
#> [53] "HPRD-phos" "HPRD_KEA"
#> [55] "HPRD_LRdb" "HPRD_MIMP"
#> [57] "HPRD_talklr" "HTRI_CollecTRI"
#> [59] "HTRIdb" "HTRIdb_DoRothEA"
#> [61] "HuRI" "ICELLNET"
#> [63] "InnateDB" "InnateDB_SignaLink3"
#> [65] "IntAct" "IntAct_CollecTRI"
#> [67] "IntAct_DoRothEA" "JASPAR_DoRothEA"
#> [69] "KEA" "KEGG-MEDICUS"
#> [71] "Kinexus_KEA" "Kirouac2010"
#> [73] "LRdb" "Li2012"
#> [75] "Lit-BM-17" "LncRNADisease"
#> [77] "MIMP" "MPPI"
#> [79] "Macrophage" "MatrixDB"
#> [81] "NCI-PID_ProtMapper" "NFIRegulomeDB_DoRothEA"
#> [83] "NRF2ome" "NTNU.Curated_CollecTRI"
#> [85] "NetPath" "NetworKIN_KEA"
#> [87] "ORegAnno" "ORegAnno_DoRothEA"
#> [89] "PAZAR_DoRothEA" "Pavlidis2021_CollecTRI"
#> [91] "PhosphoNetworks" "PhosphoPoint"
#> [93] "PhosphoSite" "PhosphoSite_KEA"
#> [95] "PhosphoSite_MIMP" "PhosphoSite_ProtMapper"
#> [97] "PhosphoSite_noref" "ProtMapper"
#> [99] "REACH_ProtMapper" "RLIMS-P_ProtMapper"
#> [101] "Ramilowski2015" "Ramilowski2015_Baccin2019"
#> [103] "ReMap_DoRothEA" "Reactome_LRdb"
#> [105] "Reactome_ProtMapper" "Reactome_SignaLink3"
#> [107] "RegNetwork_DoRothEA" "SIGNOR"
#> [109] "SIGNOR_CollecTRI" "SIGNOR_ProtMapper"
#> [111] "SPIKE" "SPIKE_LC"
#> [113] "STRING_talklr" "SignaLink3"
#> [115] "Sparser_ProtMapper" "TCRcuration_SignaLink3"
#> [117] "TFactS_CollecTRI" "TFactS_DoRothEA"
#> [119] "TFe_DoRothEA" "TRED_DoRothEA"
#> [121] "TRIP" "TRRD_DoRothEA"
#> [123] "TRRUST_CollecTRI" "TRRUST_DoRothEA"
#> [125] "TransmiR" "UniProt_LRdb"
#> [127] "Wang" "Wojtowicz2020"
#> [129] "connectomeDB2020" "dbPTM"
#> [131] "iPTMnet" "iTALK"
#> [133] "miR2Disease" "miRDeathDB"
#> [135] "miRTarBase" "miRecords"
#> [137] "ncRDeathDB" "phosphoELM"
#> [139] "phosphoELM_KEA" "phosphoELM_MIMP"
#> [141] "scConnect" "talklr"