op <- omnipath(resources = c("CA1", "SIGNOR", "SignaLink3"))
+op
+#> # A tibble: 63,078 × 15
+#> source target source_genesymbol target_genesymbol is_directed is_stimulation
+#> <chr> <chr> <chr> <chr> <dbl> <dbl>
+#> 1 Q13976 Q13507 PRKG1 TRPC3 1 0
+#> 2 Q13976 Q9HCX4 PRKG1 TRPC7 1 1
+#> 3 Q13438 Q9HBA0 OS9 TRPV4 1 1
+#> 4 P18031 Q9H1D0 PTPN1 TRPV6 1 0
+#> 5 P63244 Q9BX84 RACK1 TRPM6 1 0
+#> 6 P17612 Q9GZU1 PRKACA MCOLN1 1 0
+#> 7 Q16539 P49137 MAPK14 MAPKAPK2 1 1
+#> 8 P49137 Q13151 MAPKAPK2 HNRNPA0 1 1
+#> 9 P49137 O95453 MAPKAPK2 PARN 1 0
+#> 10 O60674 P19235 JAK2 EPOR 1 1
+#> # ℹ 63,068 more rows
+#> # ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
+#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
+#> # references <chr>, curation_effort <dbl>, n_references <int>,
+#> # n_resources <int>
+
+interactions = omnipath_interactions(
+ resources = "SignaLink3",
+ organism = 9606
+)
+
+pathways <- omnipath()
+pathways
+#> # A tibble: 81,529 × 15
+#> source target source_genesymbol target_genesymbol is_directed is_stimulation
+#> <chr> <chr> <chr> <chr> <dbl> <dbl>
+#> 1 P0DP23 P48995 CALM1 TRPC1 1 0
+#> 2 P0DP25 P48995 CALM3 TRPC1 1 0
+#> 3 P0DP24 P48995 CALM2 TRPC1 1 0
+#> 4 Q03135 P48995 CAV1 TRPC1 1 1
+#> 5 P14416 P48995 DRD2 TRPC1 1 1
+#> 6 Q99750 P48995 MDFI TRPC1 1 0
+#> 7 Q14571 P48995 ITPR2 TRPC1 1 1
+#> 8 P29966 P48995 MARCKS TRPC1 1 0
+#> 9 Q13255 P48995 GRM1 TRPC1 1 1
+#> 10 Q13586 P48995 STIM1 TRPC1 1 1
+#> # ℹ 81,519 more rows
+#> # ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
+#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
+#> # references <chr>, curation_effort <dbl>, n_references <int>,
+#> # n_resources <int>
+
+interactions <-
+ pathwayextra(
+ resources = c("BioGRID", "IntAct"),
+ organism = 9606
+ )
+
+kinase_substrate <-
+ kinaseextra(
+ resources = c('PhosphoPoint', 'PhosphoSite'),
+ organism = 9606
+ )
+
+ligand_receptor <- ligrecextra(
+ resources = c('HPRD', 'Guide2Pharma'),
+ organism = 9606
+)
+
+interactions <- post_translational(resources = "BioGRID")
+
+dorothea_grn <- dorothea(
+ resources = c('DoRothEA', 'ARACNe-GTEx_DoRothEA'),
+ organism = 9606,
+ dorothea_levels = c('A', 'B', 'C')
+)
+dorothea_grn
+#> # A tibble: 32,617 × 16
+#> source target source_genesymbol target_genesymbol is_directed is_stimulation
+#> <chr> <chr> <chr> <chr> <dbl> <dbl>
+#> 1 P01106 O14746 MYC TERT 1 1
+#> 2 P84022 P05412 SMAD3 JUN 1 1
+#> 3 Q13485 P05412 SMAD4 JUN 1 1
+#> 4 P08047 P04075 SP1 ALDOA 1 1
+#> 5 P04637 P08069 TP53 IGF1R 1 0
+#> 6 Q05516 P20248 ZBTB16 CCNA2 1 0
+#> 7 Q01196 P08700 RUNX1 IL3 1 0
+#> 8 P42224 P38936 STAT1 CDKN1A 1 1
+#> 9 P40763 P38936 STAT3 CDKN1A 1 1
+#> 10 Q04206 P08183 RELA ABCB1 1 1
+#> # ℹ 32,607 more rows
+#> # ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
+#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
+#> # references <chr>, curation_effort <dbl>, dorothea_level <chr>,
+#> # n_references <dbl>, n_resources <int>
+
+interactions <- tf_target(resources = c("DoRothEA", "SIGNOR"))
+
+grn <- transcriptional(resources = c("PAZAR", "ORegAnno", "DoRothEA"))
+#> Warning: The following resources are not available: PAZAR. Check the resource names for spelling mistakes.
+grn
+#> # A tibble: 31,896 × 16
+#> source target source_genesymbol target_genesymbol is_directed is_stimulation
+#> <chr> <chr> <chr> <chr> <dbl> <dbl>
+#> 1 P01106 O14746 MYC TERT 1 1
+#> 2 P84022 P05412 SMAD3 JUN 1 1
+#> 3 Q13485 P05412 SMAD4 JUN 1 1
+#> 4 Q04206 P25445 RELA FAS 1 1
+#> 5 P08047 P04075 SP1 ALDOA 1 1
+#> 6 P04637 P08069 TP53 IGF1R 1 0
+#> 7 Q05516 P20248 ZBTB16 CCNA2 1 0
+#> 8 Q01196 P08700 RUNX1 IL3 1 0
+#> 9 P42224 P38936 STAT1 CDKN1A 1 1
+#> 10 P40763 P38936 STAT3 CDKN1A 1 1
+#> # ℹ 31,886 more rows
+#> # ℹ 10 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
+#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
+#> # references <chr>, curation_effort <dbl>, dorothea_level <chr>,
+#> # n_references <dbl>, n_resources <int>
+
+collectri_grn <- collectri()
+collectri_grn
+#> # A tibble: 64,495 × 15
+#> source target source_genesymbol target_genesymbol is_directed is_stimulation
+#> <chr> <chr> <chr> <chr> <dbl> <dbl>
+#> 1 P01106 O14746 MYC TERT 1 1
+#> 2 P17947 P02818 SPI1 BGLAP 1 1
+#> 3 COMPLE… P05412 FOSL1_JUNB JUN 1 1
+#> 4 COMPLE… P05412 FOS_JUN JUN 1 1
+#> 5 COMPLE… P05412 FOS_JUNB JUN 1 1
+#> 6 COMPLE… P05412 FOSL2_JUND JUN 1 1
+#> 7 COMPLE… P05412 FOSL2_JUN JUN 1 1
+#> 8 COMPLE… P05412 JUN JUN 1 1
+#> 9 COMPLE… P05412 FOSB_JUNB JUN 1 1
+#> 10 COMPLE… P05412 JUNB JUN 1 1
+#> # ℹ 64,485 more rows
+#> # ℹ 9 more variables: is_inhibition <dbl>, consensus_direction <dbl>,
+#> # consensus_stimulation <dbl>, consensus_inhibition <dbl>, sources <chr>,
+#> # references <chr>, curation_effort <dbl>, n_references <dbl>,
+#> # n_resources <int>
+
+interactions <- mirna_target( resources = c("miRTarBase", "miRecords"))
+
+interactions <- tf_mirna(resources = "TransmiR")
+
+interactions <- lncrna_mrna(resources = c("ncRDeathDB"))
+
+# What are the targets of aspirin?
+interactions <- small_molecule(sources = "ASPIRIN")
+# The prostaglandin synthases:
+interactions
+#> # A tibble: 0 × 14
+#> # ℹ 14 variables: source <chr>, target <chr>, source_genesymbol <chr>,
+#> # target_genesymbol <chr>, is_directed <chr>, is_stimulation <chr>,
+#> # is_inhibition <chr>, consensus_direction <chr>,
+#> # consensus_stimulation <chr>, consensus_inhibition <chr>, sources <chr>,
+#> # references <chr>, curation_effort <chr>, n_references <lgl>
+
+interactions <- all_interactions(
+ resources = c("HPRD", "BioGRID"),
+ organism = 9606
+)
+#> Error: object 'exclude' not found
+
+