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] "DEPOD" "DIP"
#> [23] "DLRP_Cellinker" "DLRP_talklr"
#> [25] "DOMINO" "DeathDomain"
#> [27] "DoRothEA" "DoRothEA-reviews_DoRothEA"
#> [29] "ELM" "EMBRACE"
#> [31] "ENCODE-distal" "ENCODE-proximal"
#> [33] "ENCODE_tf-mirna" "FANTOM4_DoRothEA"
#> [35] "Fantom5_LRdb" "Guide2Pharma"
#> [37] "Guide2Pharma_CellPhoneDB" "Guide2Pharma_Cellinker"
#> [39] "Guide2Pharma_LRdb" "Guide2Pharma_talklr"
#> [41] "HOCOMOCO_DoRothEA" "HPMR"
#> [43] "HPMR_Cellinker" "HPMR_LRdb"
#> [45] "HPMR_talklr" "HPRD"
#> [47] "HPRD-phos" "HPRD_KEA"
#> [49] "HPRD_LRdb" "HPRD_MIMP"
#> [51] "HPRD_talklr" "HTRIdb"
#> [53] "HTRIdb_DoRothEA" "HuRI"
#> [55] "I2D_CellPhoneDB" "ICELLNET"
#> [57] "IMEx_CellPhoneDB" "InnateDB"
#> [59] "InnateDB-All_CellPhoneDB" "InnateDB_CellPhoneDB"
#> [61] "InnateDB_SignaLink3" "IntAct"
#> [63] "IntAct_CellPhoneDB" "IntAct_DoRothEA"
#> [65] "JASPAR_DoRothEA" "KEA"
#> [67] "KEGG-MEDICUS" "Kinexus_KEA"
#> [69] "Kirouac2010" "LMPID"
#> [71] "LRdb" "Li2012"
#> [73] "Lit-BM-17" "LncRNADisease"
#> [75] "MIMP" "MINT_CellPhoneDB"
#> [77] "MPPI" "Macrophage"
#> [79] "MatrixDB" "MatrixDB_CellPhoneDB"
#> [81] "NCI-PID_ProtMapper" "NFIRegulomeDB_DoRothEA"
#> [83] "NRF2ome" "NetPath"
#> [85] "NetworKIN_KEA" "ORegAnno"
#> [87] "ORegAnno_DoRothEA" "PAZAR"
#> [89] "PAZAR_DoRothEA" "PhosphoNetworks"
#> [91] "PhosphoPoint" "PhosphoSite"
#> [93] "PhosphoSite_KEA" "PhosphoSite_MIMP"
#> [95] "PhosphoSite_ProtMapper" "PhosphoSite_noref"
#> [97] "ProtMapper" "REACH_ProtMapper"
#> [99] "RLIMS-P_ProtMapper" "Ramilowski2015"
#> [101] "Ramilowski2015_Baccin2019" "ReMap_DoRothEA"
#> [103] "Reactome_LRdb" "Reactome_ProtMapper"
#> [105] "Reactome_SignaLink3" "RegNetwork_DoRothEA"
#> [107] "SIGNOR" "SIGNOR_ProtMapper"
#> [109] "SPIKE" "STRING_talklr"
#> [111] "SignaLink3" "Sparser_ProtMapper"
#> [113] "TCRcuration_SignaLink3" "TFactS_DoRothEA"
#> [115] "TFe_DoRothEA" "TRED_DoRothEA"
#> [117] "TRIP" "TRRD_DoRothEA"
#> [119] "TRRUST_DoRothEA" "TransmiR"
#> [121] "UniProt_CellPhoneDB" "UniProt_LRdb"
#> [123] "Wang" "Wojtowicz2020"
#> [125] "connectomeDB2020" "dbPTM"
#> [127] "iPTMnet" "iTALK"
#> [129] "lncrnadb" "miR2Disease"
#> [131] "miRDeathDB" "miRTarBase"
#> [133] "miRecords" "ncRDeathDB"
#> [135] "phosphoELM" "phosphoELM_KEA"
#> [137] "phosphoELM_MIMP" "scConnect"
#> [139] "talklr"