diff --git a/DESCRIPTION b/DESCRIPTION index ab74472..e935750 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -30,4 +30,4 @@ Remotes: drieslab/GiottoClass, drieslab/GiottoUtils, drieslab/Giotto@suite_modular -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.1 diff --git a/inst/Mini_datasets/seqfish/Raw/mouse_ligand_receptors.txt b/inst/Mini_datasets/seqfish/Raw/mouse_ligand_receptors.txt new file mode 100644 index 0000000..cf82b41 --- /dev/null +++ b/inst/Mini_datasets/seqfish/Raw/mouse_ligand_receptors.txt @@ -0,0 +1,1068 @@ +mouseLigand mouseReceptor +A2m Lrp1 +Aanat Mtnr1a +Aanat Mtnr1b +Adam12 Itga9 +Adam12 Itgb1 +Adam12 Sdc4 +Adam15 Itga5 +Adam15 Itga9 +Adam15 Itgb1 +Adam15 Itgb3 +Adam17 Itga5 +Adam17 Itgb1 +Adam23 Itga5 +Adam23 Itgb3 +Adam2 Itga6 +Adam2 Itgb1 +Adam9 Itga6 +Adam9 Itgav +Adam9 Itgb1 +Adam9 Itgb5 +Adcyap1 Adcyap1r1 +Adcyap1 Vipr1 +Adcyap1 Vipr2 +Adipoq Adipor1 +Adipoq Adipor2 +Adm2 Calcr +Adm2 Calcrl +Adm2 Ramp1 +Adm Calcr +Adm Calcrl +Adm Gpr182 +Adm Mrgprx2 +Adm Ramp2 +Agrn Musk +Agrp Mc3r +Agrp Mc4r +Agrp Mc5r +Agt Agtr1 +Agt Agtr2 +Agt Lrp2 +Agt Mas1 +Amh Amhr2 +Angpt1 Tek +Angpt1 Tie1 +Angpt2 Tek +Angpt4 Tek +Angptl1 Tek +Anxa1 Fpr1 +Anxa1 Fpr2 +Anxa1 Fpr3 +Apln Aplnr +Apob Ldlr +Apoe Ldlr +Apoe Lrp5 +Apoe Lrp8 +Apoe Sorl1 +Apoe Vldlr +App Fpr2 +Aregb Egfr +Areg Egfr +Arf1 Pld2 +Artn Gfra3 +Artn Ret +Asip Atrn +Asip Mc1r +Avp Avpr1a +Avp Avpr1b +Avp Avpr2 +Avp Oxtr +Bdnf Ngfr +Bdnf Ngfrap1 +Bdnf Ntrk2 +Bmp10 Acvr2a +Bmp10 Acvrl1 +Bmp10 Bmpr1a +Bmp10 Bmpr1b +Bmp10 Bmpr2 +Bmp15 Acvr2a +Bmp15 Bmpr1a +Bmp15 Bmpr1b +Bmp15 Bmpr2 +Bmp2 Acvr1 +Bmp2 Acvr2a +Bmp2 Acvr2b +Bmp2 Bmpr1a +Bmp2 Bmpr1b +Bmp2 Bmpr2 +Bmp3 Acvr2b +Bmp4 Bmpr1a +Bmp4 Bmpr1b +Bmp4 Bmpr2 +Bmp5 Bmpr1a +Bmp6 Acvr1 +Bmp6 Acvr2a +Bmp6 Bmpr1a +Bmp6 Bmpr1b +Bmp6 Bmpr2 +Bmp7 Acvr1 +Bmp7 Acvr2a +Bmp7 Acvr2b +Bmp7 Bmpr1a +Bmp7 Bmpr1b +Bmp7 Bmpr2 +Btc Egfr +Btc Erbb3 +Btc Erbb4 +Btla Tnfrsf14 +C3 C3ar1 +C3 Itgax +C3 Itgb2 +C3 Lrp1 +C5 C5ar1 +C5 C5ar2 +Calca Calcr +Calca Calcrl +Calca Ramp1 +Calcb Calcr 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+Cxcl6 Cxcr1 +Cxcl6 Cxcr2 +Cxcl9 Ccr3 +Cxcl9 Cxcr3 +Cyr61 Itga5 +Cyr61 Itgam +Cyr61 Itgb2 +Cyr61 Itgb3 +Defb4a Ccr6 +Defb4b Ccr6 +Dhh Hhip +Dhh Ptch2 +Dkk1 Kremen1 +Dkk1 Kremen2 +Dkk1 Lrp6 +Dkk2 Lrp6 +Dlk1 Notch1 +Dll1 Notch1 +Dll1 Notch2 +Dll1 Notch3 +Dll4 Notch1 +Dll4 Notch2 +Dll4 Notch3 +Dll4 Notch4 +Eda Eda2r +Eda Edar +Edn1 Ednra +Edn2 Ednra +Edn3 Ednrb +Efna1 Epha1 +Efna1 Epha2 +Efna1 Epha3 +Efna1 Epha4 +Efna1 Epha5 +Efna1 Epha6 +Efna1 Epha7 +Efna1 Epha8 +Efna2 Epha2 +Efna2 Epha3 +Efna2 Epha4 +Efna2 Epha5 +Efna2 Epha6 +Efna2 Epha7 +Efna2 Epha8 +Efna3 Epha1 +Efna3 Epha2 +Efna3 Epha3 +Efna3 Epha4 +Efna3 Epha5 +Efna3 Epha6 +Efna3 Epha7 +Efna3 Epha8 +Efna3 Ephb1 +Efna4 Epha2 +Efna4 Epha3 +Efna4 Epha4 +Efna4 Epha5 +Efna4 Epha6 +Efna4 Epha7 +Efna4 Epha8 +Efna5 Epha2 +Efna5 Epha3 +Efna5 Epha4 +Efna5 Epha5 +Efna5 Epha6 +Efna5 Epha7 +Efna5 Epha8 +Efna5 Ephb2 +Efnb1 Ephb1 +Efnb1 Ephb2 +Efnb1 Ephb3 +Efnb1 Ephb4 +Efnb1 Ephb6 +Efnb2 Epha4 +Efnb2 Ephb1 +Efnb2 Ephb2 +Efnb2 Ephb3 +Efnb2 Ephb4 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Itgam +Icam4 Itgav +Icam4 Itgb2 +Icam4 Itgb3 +Icam5 Itgal +Icam5 Itgb2 +Ifna10 Ifnar1 +Ifna10 Ifnar2 +Ifna13 Ifnar1 +Ifna13 Ifnar2 +Ifna14 Ifnar1 +Ifna14 Ifnar2 +Ifna16 Ifnar1 +Ifna16 Ifnar2 +Ifna17 Ifnar1 +Ifna17 Ifnar2 +Ifna1 Ifnar1 +Ifna1 Ifnar2 +Ifna21 Ifnar1 +Ifna21 Ifnar2 +Ifna2 Ifnar1 +Ifna2 Ifnar2 +Ifna4 Ifnar1 +Ifna4 Ifnar2 +Ifna5 Ifnar1 +Ifna5 Ifnar2 +Ifna6 Ifnar1 +Ifna6 Ifnar2 +Ifna7 Ifnar1 +Ifna7 Ifnar2 +Ifna8 Ifnar1 +Ifna8 Ifnar2 +Ifnb1 Ifnar1 +Ifnb1 Ifnar2 +Ifng Ifngr1 +Ifng Ifngr2 +Ifnl1 Ifnlr1 +Ifnl1 Il10rb +Ifnl2 Ifnlr1 +Ifnl2 Il10rb +Ifnl3 Ifnlr1 +Ifnl3 Il10rb +Ifnw1 Ifnar1 +Ifnw1 Ifnar2 +Igf1 Igf1r +Igf2 Igf1r +Igf2 Igf2r +Igf2 Insr +Ihh Hhip +Ihh Ptch1 +Il10 Il10ra +Il10 Il10rb +Il11 Il11ra +Il11 Il6st +Il12a Il12rb1 +Il12a Il12rb2 +Il12b Il12rb1 +Il12b Il12rb2 +Il13 Il13ra1 +Il13 Il13ra2 +Il13 Il2rg +Il13 Il4r +Il15 Il15ra +Il15 Il2rb +Il15 Il2rg +Il16 Cd4 +Il17a Il17ra +Il17b Il17rb +Il18 Il18r1 +Il18 Il18rap +Il18 Il1rapl1 +Il19 Il20ra +Il19 Il20rb +Il1a Il1r1 +Il1a Il1r2 +Il1b Il1r1 +Il1b Il1r2 +Il1b Il1rap +Il1rn Il1r1 +Il1rn Il1r2 +Il20 Il20ra +Il20 Il20rb +Il20 Il22ra1 +Il21 Il21r +Il21 Il2rg +Il22 Il10ra +Il22 Il22ra1 +Il22 Il22ra2 +Il23a Il12rb1 +Il23a Il23r +Il24 Il20ra +Il24 Il20rb +Il24 Il22ra1 +Il25 Il17rb +Il2 Il2ra +Il2 Il2rb +Il2 Il2rg +Il31 Il31ra +Il31 Osmr +Il3 Csf2rb +Il3 Il3ra +Il4 Il13ra1 +Il4 Il2rg +Il4 Il4r +Il5 Csf2rb +Il5 Il5ra +Il6 Il6r +Il6 Il6st +Il7 Il2rg +Il7 Il7r +Il8 Cxcr1 +Il8 Cxcr2 +Il8 Darc +Il9 Il2rg +Il9 Il9r +Inha Acvr2a +Inha Tgfbr3 +Inhba Acvr1 +Inhba Acvr1b +Inhba Acvr2a +Inhba Acvr2b +Inhba Bambi +Inhbb Acvr1 +Inhbb Acvr1b +Inhbb Acvr2a +Inhbb Acvr2b +Inhbc Acvr1 +Inhbc Acvr1b +Inhbc Acvr2a +Inhbc Acvr2b +Insl3 Rxfp2 +Insl5 Rxfp3 +Insl5 Rxfp4 +Ins Insr +Jag1 Notch1 +Jag1 Notch2 +Jag1 Notch3 +Jag1 Notch4 +Jag2 Notch1 +Jag2 Notch2 +Jag2 Notch3 +Kiss1 Kiss1r +Kitlg Kit +Kng1 Bdkrb1 +Kng1 Bdkrb2 +Kng1 Gpr135 +Lama1 Itga7 +Lama1 Itgb1 +Lama1 Itgb8 +Lama1 Rpsa +Lama2 Itga7 +Lama2 Itgb1 +Lama2 Rpsa +Lamb1 Itga6 +Lamb1 Itgb1 +Lamb2 Rpsa +Lamc2 Itga3 +Lamc2 Itga6 +Lamc2 Itgb1 +Lamc2 Itgb4 +Lefty2 Acvr2b +Lep Lepr +Lhb Lhcgr +Lif Il6st +Lif Lifr +Liph Lpar1 +Liph Lpar2 +Liph Lpar4 +Lrpap1 Lrp1 +Lta Ltbr +Lta Tnfrsf14 +Lta Tnfrsf1a +Lta Tnfrsf1b +Ltb Cd40 +Ltb Ltbr +Ltf Lrp1 +Ltf Lrp11 +Madcam1 Itga4 +Madcam1 Itgb7 +Mdk Alk +Mdk Ptprz1 +Mln Mlnr +Mmp13 Lrp1 +Mmp9 Lrp1 +Mst1 Mst1r +Nampt Insr +Ncam1 Robo1 +Ncam1 Robo3 +Ndp Fzd4 +Ndp Lgr4 +Ngf Ngfr +Ngf Ntrk1 +Ngf Sort1 +Nid1 Ptprf +Nlgn1 Nrxn1 +Nlgn1 Nrxn3 +Nlgn2 Nrxn1 +Nlgn2 Nrxn2 +Nlgn2 Nrxn3 +Nlgn3 Nrxn1 +Nlgn3 Nrxn2 +Nlgn3 Nrxn3 +Nmb Grpr +Nmb Nmbr +Nms Nmur1 +Nms Nmur2 +Nmu Nmur1 +Nmu Nmur2 +Nodal Acvr1b +Nodal Acvr1c +Nodal Acvr2a +Nodal Acvr2b +Nov Notch1 +Npb Npbwr1 +Npb Npbwr2 +Npff Npffr1 +Npff Npffr2 +Npnt Itga8 +Npnt Itgb1 +Nppa Npr1 +Nppa Npr3 +Nppb Npr1 +Nppb Npr2 +Nppb Npr3 +Nppc Npr2 +Nps Npsr1 +Npvf Npffr1 +Npvf Npffr2 +Npw Npbwr1 +Npw Npbwr2 +Npy Npy1r +Npy Npy2r +Npy Npy4r +Npy Npy5r +Npy Prlhr +Nrg1 Erbb2 +Nrg1 Erbb3 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