Transfer tool to new repo

nvaulin · May 21, 2023 · ed96ee3 · ed96ee3
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diff --git a/Databases/MetaCyc_pathways_by_species.csv b/Databases/MetaCyc_pathways_by_species.csv
diff --git a/Databases/cystic_fibrosis/Images/clustermap.png b/Databases/cystic_fibrosis/Images/clustermap.png
diff --git a/Databases/cystic_fibrosis/Images/cv_bg_correlation_distributions.png b/Databases/cystic_fibrosis/Images/cv_bg_correlation_distributions.png
diff --git a/Databases/cystic_fibrosis/Images/cv_correlation_distribution.png b/Databases/cystic_fibrosis/Images/cv_correlation_distribution.png
diff --git a/Databases/cystic_fibrosis/Images/metabolite_cluster_consensus.png b/Databases/cystic_fibrosis/Images/metabolite_cluster_consensus.png
diff --git a/Databases/cystic_fibrosis/Images/microbe_cluster_consensus.png b/Databases/cystic_fibrosis/Images/microbe_cluster_consensus.png
diff --git a/Databases/cystic_fibrosis/Images/top_correlated_metabolites.png b/Databases/cystic_fibrosis/Images/top_correlated_metabolites.png
diff --git a/Databases/cystic_fibrosis/cv_correlations.csv b/Databases/cystic_fibrosis/cv_correlations.csv
diff --git a/Databases/cystic_fibrosis/final_network_model.h5 b/Databases/cystic_fibrosis/final_network_model.h5
diff --git a/Databases/cystic_fibrosis/interaction_score_matrix.csv b/Databases/cystic_fibrosis/interaction_score_matrix.csv
diff --git a/Databases/cystic_fibrosis/metabolite_cluster_matrix.csv b/Databases/cystic_fibrosis/metabolite_cluster_matrix.csv
diff --git a/Databases/cystic_fibrosis/metabolite_clusters.csv b/Databases/cystic_fibrosis/metabolite_clusters.csv
@@ -0,0 +1,145 @@
+,metab_name
+0,Nortriptyline
+1,NHQ
+2,Indole-2-carboxylic acid
+3,MLS000736964-01!
+4,PQS/HQNO
+5,2-Heptyl-4-hydroxyquinoline N-oxide
+6,19-Norepiandrosterone
+7,16.beta.-Hydroxyfurazabol
+8,"(2S,3S)-(-)-3-Phenylglycidol"
+9,MLS001401453-01!ZOLPIDEM TARTRATE
+10,MLS000737174-01!
+11,"1(6H)-Pyridazinebutanoic acid, 6-imino-3-(4-methoxyphenyl)-"
+12,3-Phenoxypropionic acid
+13,4-(1-Piperazinyl)-1H-indole
+14, Lyso-Sphingomyelin 
+15,"2-Methylamino-1-(3,4-methylenedioxyphenyl)propan-1-one"
+16,Gliotoxin
+17,3-(2-Hydroxyethyl)indole
+18,Rha-Rha-C10-C10 (M+H)
+19,Massbank:FIO00114 Harman
+20,Phenazine-1-carboxylic Acid
+21,2-Hydroxy-7-methylquinoline-3-carbaldehyde
+22, 1-Hexadecanoyl-2-(9Z-octadecenoyl)-sn-glycero-3-phosphoethanolamine 
+23,PC(0:0/18:0);  C26H55N1O7P1
+24, Sertraline 
+25,Norbolethone
+26,Pyochelin
+27,2-Hydroxy-6-methylquinoline-3-carbaldehyde
+28,"NCGC00380742-01_C22H25N3O3_9-Methoxy-12-(2-methyl-1-propen-1-yl)-1,2,3,5a,6,11,12,14a-octahydro-5H,14H-pyrrolo[1'',2'':4',5']pyrazino[1',2':1,6]pyrido[3,4-b]indole-5,14-dione"
+29,L-Tryptophan
+30, Lyso-PC(16:0) 
+31,"NCGC00385669-01!(E)-3-(acetyloxymethyl)-5-(2-formyl-4-hydroxy-5,5,8a-trimethyl-1,4,4a,6,7,8-hexahydronaphthalen-1-yl)pent-2-enoic acid"
+32,"1H-Indole-3-carboxylic acid, 1-(cyclohexylmethyl)-"
+33,L-Tryptophanamide
+34,Coproporphyrin I
+35, Palmitoylcarnitine 
+36, DL-Indole-3-lactic acid 
+37, Dibutyl phthalate 
+38,Aztreonam
+39,"C9:db-PQS, C9:DB-NQNO"
+40,1-O-Octadecyl-sn-glyceryl-3-phosphorylcholine
+41,Azithromycin
+42,Tyr-Trp
+43, 1-(1Z-Octadecenyl)-sn-glycero-3-phosphocholine 
+44,4-(p-Methoxyphenyl)-2-butanone
+45,"NCGC00169614-02_C24H21N5O4_(1S,3S,12S,14R,27S)-12-Hydroxy-1,3-dimethyl-2,5,15,23,25-pentaazaheptacyclo[12.10.2.1~2,5~.0~6,11~.0~12,27~.0~15,24~.0~17,22~]heptacosa-6,8,10,17,19,21,23-heptaene-4,16,26-trione"
+46,PC(20:0/20:4);  C48H89N1O8P1
+47," 1,2-Diarachidonoyl-sn-glycero-3-phosphocholine "
+48,"Massbank:UF408702 Sulfamethoxazole|4-amino-N-(5-methyl-1,2-oxazol-3-yl)benzenesulfonamide"
+49,cis-Vaccenic acid
+50," Inosine, 2'-deoxy- "
+51,"NCGC00385123-01_C22H30O6_7b,9-Dihydroxy-3-(hydroxymethyl)-1,1,6,8-tetramethyl-5-oxo-1,1a,1b,4,4a,5,7a,7b,8,9-decahydro-9aH-cyclopropa[3,4]benzo[1,2-e]azulen-9a-yl acetate"
+52, Tris(2-butoxyethyl) phosphate 
+53, Harmane 
+54," 1-Octadecanoyl-2-(4Z,7Z,10Z,13Z,16Z,19Z-docosahexaenoyl)-sn-glycero-3-phosphocholine "
+55, 1-Octadecyl-sn-glycero-3-phosphocholine 
+56, 1-Stearoyl-2-hydroxy-sn-glycero-3-phosphocholine 
+57, Abrine 
+58, Azithromycin 
+59, 1-(1Z-Hexadecenyl)-sn-glycero-3-phosphocholine 
+60,Ivacaftor
+61,Eicosanoids_12-oxoETE_C20H30O3
+62,(-)-Riboflavin
+63,"5S-Hydroxy-6E,8Z,11Z-eicosatrienoic acid"
+64, 1-Behenoyl-2-hydroxy-sn-glycero-3-phosphocholine 
+65, Phe-Pro 
+66,"10E,12Z-octadecadienoic acid"
+67,1-Stearoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine
+68,DescladinoseAzithromycin
+69,SM(d18:1/25:0);  C48H98N2O6P1
+70,Octocrylene
+71,.gamma.-Phenyl-.gamma.-butyrolactone
+72, Glu-Phe 
+73,7-Oxocholesterol
+74, 1-(9Z-Octadecenoyl)-sn-glycero-3-phosphocholine 
+75,"2,3-Methylenedioxymethcathinone"
+76,"1,2-Dimethoxy-4-(2-propenyl)benzene"
+77,PC(18:1/20:5);  C46H81N1O8P1
+78,"NCGC00385811-01!6-[3-[(3,4-dimethoxyphenyl)methyl]-4-methoxy-2-(methoxymethyl)butyl]-4-methoxy-1,3-benzodioxole"
+79, N-Tetracosanoyl-4-sphingenyl-1-O-phosphorylcholine 
+80,3-Hydroxymethylmefenamic acid
+81,1-O-Hexadecyl-2-O-acetyl-sn-glyceryl-3-phosphorylcholine
+82,NHQ_C9:db
+83," 1,2-Diheptadecanoyl-sn-glycero-3-phosphocholine "
+84,"1,2-dioleoyl-sn-glycero-3-phosphatidylcholine"
+85,Gly-Phe
+86, Sulfadimethoxine 
+87, Coproporphyrin I 
+88,NCGC00380283-01!4-[5-[[4-[5-[acetyl(hydroxy)amino]pentylamino]-4-oxobutanoyl]-hydroxyamino]pentylamino]-4-oxobutanoic acid
+89, 1-Palmitoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine 
+90, Ethenzamide 
+91,PC(O-18:0/18:1);  C44H89N1O7P1
+92,N-(3-(Aminomethyl)benzyl)acetamidine
+93,MLS000777209-01!phenazine-1-carboxylic acid
+94,Massbank:FIO00571 Caffeine
+95,2-(4-Acetylpyridin-2-yl)benzonitrile
+96," 1,2-Dipalmitoleoyl-sn-glycero-3-phosphocholine "
+97,D-erythro-C18-Sphingosine
+98, PAF C-16 
+99, 1-Arachidoyl-2-hydroxy-sn-glycero-3-phosphocholine 
+100,"2,6-Di-tert-butyl-4-hydroxymethylphenol"
+101, 1-Lignoceroyl-2-hydroxy-sn-glycero-3-phosphocholine 
+102, 1-Oleoyl-2-palmitoyl-sn-glycero-3-phosphocholine 
+103,"NCGC00385199-01!2-[3,4-bis[[(2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy]phenyl]-5,7-dihydroxychromen-4-one"
+104,19-Hydroxycholesterol
+105,Putative Contaminant
+106,NCGC00180497-02!
+107,1-Eicosatrienoyl-sn-glycero-3-phosphoethanolamine
+108,Lumisterol 3
+109,1-Oleoyl-2-hydroxy-sn-glycero-3-phospho-(1'-rac-glycerol)
+110, 1-Myristoyl-sn-glycero-3-phosphocholine 
+111,LysoPAF
+112, 3-Indoleacetic acid 
+113, 1-Stearoyl-2-linoleoyl-sn-glycero-3-phosphocholine 
+114,GalNAcbeta1-3Galalpha1-3Galbeta1-4Glcbeta-Cer(d18:1/16:0)
+115, 1-Myristoyl-2-stearoyl-sn-glycero-3-phosphocholine 
+116,PC(16:0/18:0);  C42H85N1O8P1
+117,2-Hydroxyphenethyl alcohol
+118,PC(16:0/20:1);  C44H87N1O8P1
+119, 1-Hexadecanoyl-sn-glycero-3-phosphocholine 
+120, 1-Stearoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine 
+121,Guanosine
+122, 1-Linoleoylglycerol 
+123,MLS001332469-01!D-Sphingosine123-78-4
+124,SM(d18:2/16:0);  C39H78N2O6P1
+125,Ethyl 4-hydroxyquinoline-2-carboxylate
+126,PC(18:1/22:4);  C48H87N1O8P1
+127,18:1(2S-OH) Ceramide
+128,"Massbank:EA019911 Trimethoprim|2,4-Diamino-5-(3,4,5-trimethoxybenzyl)pyrimidine|5-[(3,4,5-trimethoxyphenyl)methyl]pyrimidine-2,4-diamine"
+129,SM(d19:1/24:0);  C48H98N2O6P1
+130, D-erythro-C18-Sphingosine 
+131,HHQ
+132,2-(9H-Xanthen-9-yl)-malonic acid
+133,PC(15:0/16:0);  C39H79N1O8P1
+134,Massbank:PR040237 4-Methoxycinnamic acid|3-(4-methoxyphenyl)prop-2-enoic acid
+135,UHQ (mixed MS2 C11:db:UHQ)
+136,C11:DB UHQ aka  2-undecenyl-quinoloin-4(1H)-one position of double bond unknown
+137,1-Hexadecyl-sn-glycero-3-phosphocholine
+138,C17-Sphinganine
+139,PC(O-18:1/20:4);  C46H85N1O7P1
+140,PC(17:0/18:1);  C43H85N1O8P1
+141,phenylethylamide 359
+142,Verruculogen
+143,PC(O-16:0/O-16:0);  C40H85N1O6P1