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  "Title": "METabolomics pre-PRocessing, functiOnal analysis and\nVIZualisation",
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  "Description": "MetaProViz can analyse standard metabolomics and\nexometabolomics data (CoRe). It performs pre-processing\nincluding feature filtering, missing value imputation,\nnormalisation and outlier detection. It performs functional\nanalysis including differential metabolite analysis (DMA),\nclustering based on regulatory rules (MCA) and contains\ndifferent visualisation methods to extract biological\ninterpretable graphs and saves them in a publication ready\nformat.",
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  "Date/Publication": "2026-04-28 13:06:33 UTC",
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        "homoarginine",
        "hypotaurine",
        "hypoxanthine",
        "IMP",
        "indole",
        "indole-3-lactate",
        "inosine",
        "isoleucine",
        "isovalerylcarnitine",
        "KMV",
        "lactate",
        "leucine",
        "lysine",
        "malate",
        "malonate",
        "malonylcarnitine C3-DC",
        "mesaconate",
        "methionine",
        "methionine sulfoxide",
        "methylhistidine",
        "methylindole",
        "methylmalonylcarnitine C3-DC-M/succinylcarnitine C4-DC",
        "mevalonic acid 5-pyrophosphate",
        "myo-inositol",
        "N-acetylalanine",
        "N-acetylarginine",
        "N-acetylaspartate",
        "N-acetylaspartylglutamate",
        "N-acetylglutamate",
        "N-acetylglutamine",
        "N-acetylhexosamine phosphate",
        "N-acetylhistidine",
        "N-acetylmethionine",
        "N-acetylneuramic acid",
        "N-acetylornithine",
        "N-acetylserine",
        "NAD",
        "NADH",
        "NADP",
        "NADPH",
        "N-carbamoylaspartate",
        "ophthalmate",
        "ornithine",
        "orotate",
        "orotidine",
        "pantothenate",
        "pentose phosphates",
        "phenylalanine",
        "phosphocreatine",
        "phosphoenolpyruvate",
        "phosphoethanolamine",
        "phosphorylcholine",
        "proline",
        "propionylcarnitine",
        "pyroglutamic acid",
        "pyruvate",
        "S-(2-succinyl)cysteine",
        "S-adenosylhomocysteine",
        "S-adenosylmethionine",
        "SAICAR",
        "sedoheptulose 7-phosphate",
        "serine",
        "S-lactoylglutathione",
        "stearoylcarnitine C18",
        "succinate",
        "succinylglutathione",
        "taurine",
        "tetradecanoylcarnitine C14",
        "tetradecenoylcarnitine C14:1",
        "thiamine",
        "threonine",
        "trans-4-hydroxyproline",
        "trimethyllysine",
        "tryptophan",
        "tyrosine",
        "UDP",
        "UDP-GlcNac",
        "UDP-hexose",
        "UMP",
        "uric acid",
        "uridine",
        "UTP",
        "valine",
        "Val-Lys",
        "xanthine"
      ],
      "rows": 58,
      "table": true,
      "tojson": true
    },
    {
      "name": "intracell_raw_se",
      "title": "intracell_raw_se",
      "object": "intracell_raw_se",
      "file": "intracell_raw_se.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "mca_core_rules",
      "title": "mca_core_rules",
      "object": "mca_core_rules",
      "file": "mca_core_rules.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Intra",
        "CoRe",
        "Core_Direction",
        "RG1_All",
        "R2_Significant",
        "RG3_Change",
        "RG3_ChangeNum"
      ],
      "rows": 108,
      "table": true,
      "tojson": true
    },
    {
      "name": "mca_twocond_rules",
      "title": "mca_twocond_rules",
      "object": "mca_twocond_rules",
      "file": "mca_twocond_rules.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Cond1",
        "Cond2",
        "RG1_All",
        "RG2_Significant",
        "RG3_SignificantChange"
      ],
      "rows": 36,
      "table": true,
      "tojson": true
    },
    {
      "name": "medium_raw",
      "title": "medium_raw",
      "object": "medium_raw",
      "file": "medium_raw.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Code",
        "Conditions",
        "Biological_Replicates",
        "GrowthFactor",
        "valine-d8",
        "hipppuric acid-d5",
        "2-hydroxyglutarate",
        "2-ketoglutarate",
        "3-Dehydro-L-threonate",
        "acetylcarnitine",
        "acetylcholine",
        "acetylornithine",
        "aconitate",
        "alanine",
        "arginine",
        "asparagine",
        "aspartate",
        "betaine",
        "butyryl-carnitine",
        "carbamoyl phosphate",
        "carnitine",
        "citrulline",
        "creatine",
        "creatinine",
        "cystine",
        "dihydroorotate",
        "fumarate",
        "gluconate",
        "glucose",
        "glutamate",
        "glutamine",
        "glycerylphosphorylcholine",
        "glycine",
        "histidine",
        "hydroxyphenyllactic acid",
        "hydroxyphenylpyruvate",
        "hydroxyproline",
        "hypotaurine",
        "hypoxanthine",
        "isovalerylcarnitine",
        "KMV+KIC",
        "lactate",
        "leucine+isoleucine",
        "linoleic acid",
        "lysine",
        "malate",
        "methionine",
        "methylarginine",
        "methylaspartate",
        "myo-inositol",
        "N-acetylaspartate",
        "N-acetylaspartylglutamate",
        "N-acetylglutamate",
        "N-acetylneuramic acid",
        "oleic acid",
        "ornithine",
        "orotate",
        "palmitate",
        "pantothenate",
        "phenylalanine",
        "phosphocholine",
        "proline",
        "propionylcarnitine",
        "pyroglutamic-acid",
        "pyruvate",
        "S-(2-succinyl)cysteine",
        "serine",
        "stearic acid",
        "succinate",
        "succinyladenosine",
        "taurine",
        "threonine",
        "tryptophan",
        "tyrosine",
        "uric acid",
        "valine",
        "xanthine"
      ],
      "rows": 44,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_dma",
      "title": "tissue_dma",
      "object": "tissue_dma",
      "file": "tissue_dma.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Metabolite",
        "Log2FC",
        "AveExpr",
        "t.val",
        "p.val",
        "p.adj",
        "B",
        "SUPER_PATHWAY",
        "SUB_PATHWAY",
        "COMP_ID",
        "PLATFORM",
        "RI",
        "MASS",
        "CAS",
        "PUBCHEM",
        "KEGG",
        "Group_HMDB"
      ],
      "rows": 570,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_dma_old",
      "title": "tissue_dma_old",
      "object": "tissue_dma_old",
      "file": "tissue_dma_old.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Metabolite",
        "Log2FC",
        "AveExpr",
        "t.val",
        "p.val",
        "p.adj",
        "B",
        "SUPER_PATHWAY",
        "SUB_PATHWAY",
        "COMP_ID",
        "PLATFORM",
        "RI",
        "MASS",
        "CAS",
        "PUBCHEM",
        "KEGG",
        "Group_HMDB"
      ],
      "rows": 570,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_dma_young",
      "title": "tissue_dma_young",
      "object": "tissue_dma_young",
      "file": "tissue_dma_young.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Metabolite",
        "Log2FC",
        "AveExpr",
        "t.val",
        "p.val",
        "p.adj",
        "B",
        "SUPER_PATHWAY",
        "SUB_PATHWAY",
        "COMP_ID",
        "PLATFORM",
        "RI",
        "MASS",
        "CAS",
        "PUBCHEM",
        "KEGG",
        "Group_HMDB"
      ],
      "rows": 570,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_meta",
      "title": "Tissue_Metadata",
      "object": "tissue_meta",
      "file": "tissue_meta.rda",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Metabolite",
        "CAS",
        "SUPER_PATHWAY",
        "SUB_PATHWAY",
        "COMP_ID",
        "PLATFORM",
        "RI",
        "MASS",
        "PUBCHEM",
        "KEGG",
        "HMDB"
      ],
      "rows": 877,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_norm",
      "title": "tissue_norm",
      "object": "tissue_norm",
      "file": "tissue_norm.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Code",
        "CLIENT_IDENTIFIER",
        "TISSUE_TYPE",
        "MATCHING_INDEX",
        "GENDER",
        "RACE",
        "AGE_AT_SURGERY",
        "PATHSTAGET_1",
        "TYPE-STAGE",
        "PATHSTAGEN_1",
        "PATHSTAGEM_1",
        "PATHGRADE1",
        "STAGE",
        "AGE",
        "1,2-propanediol",
        "1,3-dihydroxyacetone",
        "1,5-anhydroglucitol (1,5-AG)",
        "10-heptadecenoate (17:1n7)",
        "10-nonadecenoate (19:1n9)",
        "13-HODE + 9-HODE",
        "15-methylpalmitate (isobar with 2-methylpalmitate)",
        "16-hydroxypalmitate",
        "1-arachidonoylglycerophosphocholine*",
        "1-arachidonoylglycerophosphoethanolamine*",
        "1-arachidonoylglycerophosphoinositol*",
        "1-arachidonylglycerol",
        "1-docosahexaenoylglycerophosphocholine*",
        "1-heptadecanoylglycerophosphocholine",
        "1-heptadecanoylglycerophosphoethanolamine*",
        "1-linoleoylglycerol (1-monolinolein)",
        "1-linoleoylglycerophosphocholine",
        "1-linoleoylglycerophosphoethanolamine*",
        "1-methylimidazoleacetate",
        "1-myristoylglycerophosphocholine",
        "1-myristoylglycerophosphoethanolamine",
        "1-oleoylglycerol (1-monoolein)",
        "1-oleoylglycerophosphocholine",
        "1-oleoylglycerophosphoethanolamine",
        "1-oleoylglycerophosphoinositol*",
        "1-oleoylglycerophosphoserine",
        "1-palmitoleoylglycerophosphocholine*",
        "1-palmitoleoylglycerophosphoethanolamine*",
        "1-palmitoylglycerol (1-monopalmitin)",
        "1-palmitoylglycerophosphocholine",
        "1-palmitoylglycerophosphoethanolamine",
        "1-palmitoylglycerophosphoinositol*",
        "1-palmitoylplasmenylethanolamine*",
        "1-pentadecanoylglycerophosphocholine*",
        "1-stearoylglycerol (1-monostearin)",
        "1-stearoylglycerophosphocholine",
        "1-stearoylglycerophosphoethanolamine",
        "1-stearoylglycerophosphoinositol",
        "2-aminoadipate",
        "2-aminobutyrate",
        "2-arachidonoylglycerophosphocholine*",
        "2-arachidonoylglycerophosphoethanolamine*",
        "2'-deoxyadenosine 3'-monophosphate",
        "2'-deoxycytidine 3'-monophosphate",
        "2'-deoxyguanosine",
        "2'-deoxyinosine",
        "2-docosahexaenoylglycerophosphocholine*",
        "2-docosahexaenoylglycerophosphoethanolamine*",
        "2-docosapentaenoylglycerophosphocholine*",
        "2-docosapentaenoylglycerophosphoethanolamine*",
        "2-eicosatrienoylglycerophosphocholine*",
        "2-ethylhexanoate",
        "2-hydroxyacetaminophen sulfate*",
        "2-hydroxybutyrate (AHB)",
        "2-hydroxyglutarate",
        "2-hydroxyhippurate (salicylurate)",
        "2-hydroxyisobutyrate",
        "2-hydroxypalmitate",
        "2-isopropylmalate",
        "2-linoleoylglycerol (2-monolinolein)",
        "2-linoleoylglycerophosphocholine*",
        "2-linoleoylglycerophosphoethanolamine*",
        "2-methylbutyroylcarnitine",
        "2-myristoylglycerophosphocholine*",
        "2-oleoylglycerol (2-monoolein)",
        "2-oleoylglycerophosphocholine*",
        "2-oleoylglycerophosphoethanolamine*",
        "2-oleoylglycerophosphoserine*",
        "2-palmitoleoylglycerophosphocholine*",
        "2-palmitoylglycerol (2-monopalmitin)",
        "2-palmitoylglycerophosphocholine*",
        "2-palmitoylglycerophosphoethanolamine*",
        "2-phosphoglycerate",
        "2-stearoylglycerophosphocholine*",
        "2-stearoylglycerophosphoethanolamine*",
        "3-(4-hydroxyphenyl)lactate",
        "3-(cystein-S-yl)acetaminophen*",
        "3-(N-acetyl-L-cystein-S-yl) acetaminophen*",
        "3,4-dihydroxyphenethyleneglycol",
        "3-aminoisobutyrate",
        "3-carboxy-4-methyl-5-propyl-2-furanpropanoate (CMPF)",
        "3-dehydrocarnitine*",
        "3'-dephosphocoenzyme A",
        "3-hydroxybutyrate (BHBA)",
        "3-hydroxydecanoate",
        "3-hydroxyhippurate",
        "3-hydroxyoctanoate",
        "3-indoxyl sulfate",
        "3-methyl-2-oxovalerate",
        "3-methylhistidine",
        "3-phosphoglycerate",
        "3-ureidopropionate",
        "4-acetamidophenol",
        "4-acetaminophen sulfate",
        "4-androsten-3beta,17beta-diol disulfate 1*",
        "4-guanidinobutanoate",
        "4-hydroxybutyrate (GHB)",
        "4-hydroxyglutamate",
        "4-hydroxyhippurate",
        "4-hydroxyphenylacetate",
        "4-methyl-2-oxopentanoate",
        "5,6-dihydrouracil",
        "5-aminovalerate",
        "5-HETE",
        "5-methyltetrahydrofolate (5MeTHF)",
        "5-methylthioadenosine (MTA)",
        "5-methyluridine (ribothymidine)",
        "5-oxoETE",
        "5-oxoproline",
        "6-keto prostaglandin F1alpha",
        "6-phosphogluconate",
        "6'-sialyllactose",
        "7-alpha-hydroxy-3-oxo-4-cholestenoate (7-Hoca)",
        "7-alpha-hydroxycholesterol",
        "7-beta-hydroxycholesterol",
        "acetylcarnitine",
        "Ac-Ser-Asp-Lys-Pro-OH",
        "adenine",
        "adenosine",
        "adenosine 2'-monophosphate (2'-AMP)",
        "adenosine 3'-monophosphate (3'-AMP)",
        "adenosine 5'-monophosphate (AMP)",
        "adenylosuccinate",
        "adipate",
        "adrenate (22:4n6)",
        "agmatine",
        "alanine",
        "alanylalanine",
        "alanylglutamate",
        "alanylglycine",
        "alanylisoleucine",
        "alanylleucine",
        "alanylmethionine",
        "alanylphenylalanine",
        "alanylthreonine",
        "alanyltryptophan",
        "alanyltyrosine",
        "alanylvaline",
        "allo-threonine",
        "alpha-glutamylglutamate",
        "alpha-glutamyltryptophan",
        "alpha-glutamyltyrosine",
        "alpha-hydroxyisovalerate",
        "alpha-tocopherol",
        "androsterone sulfate",
        "anserine",
        "arabitol",
        "arabonate",
        "arachidate (20:0)",
        "arachidonate (20:4n6)",
        "arginine",
        "argininosuccinate",
        "arginylleucine",
        "arginylmethionine",
        "arginylphenylalanine",
        "arginyltyrosine",
        "arginylvaline",
        "ascorbate (Vitamin C)",
        "asparagine",
        "aspartate",
        "aspartate-glutamate",
        "aspartylleucine",
        "aspartylphenylalanine",
        "aspartyltryptophan",
        "aspartylvaline",
        "atenolol",
        "azelate (nonanedioate)",
        "benzoate",
        "beta-alanine",
        "beta-hydroxypyruvate",
        "betaine",
        "beta-tocopherol",
        "bilirubin (E,E)*",
        "bilirubin (Z,Z)",
        "butyrylcarnitine",
        "caprate (10:0)",
        "caproate (6:0)",
        "caprylate (8:0)",
        "carnitine",
        "catechol sulfate",
        "celecoxib",
        "C-glycosyltryptophan*",
        "chiro-inositol",
        "cholate",
        "cholesterol",
        "choline",
        "choline phosphate",
        "cinnamoylglycine",
        "cis-aconitate",
        "cis-vaccenate (18:1n7)",
        "citalopram",
        "citramalate",
        "citrate",
        "citrulline",
        "codeine",
        "cortisol",
        "cortisone",
        "creatine",
        "creatinine",
        "cysteine",
        "cysteine-glutathione disulfide",
        "cysteinylglycine",
        "cystine",
        "cytidine",
        "cytidine 5'-diphosphocholine",
        "cytidine 5'-monophosphate (5'-CMP)",
        "cytidine-3'-monophosphate (3'-CMP)",
        "cytosine-2',3'-cyclic monophosphate",
        "deoxycarnitine",
        "dihomo-linoleate (20:2n6)",
        "dihomo-linolenate (20:3n3 or n6)",
        "dihydrocholesterol",
        "dimethylarginine (SDMA + ADMA)",
        "dimethylglycine",
        "docosadienoate (22:2n6)",
        "docosahexaenoate (DHA; 22:6n3)",
        "docosapentaenoate (n3 DPA; 22:5n3)",
        "docosapentaenoate (n6 DPA; 22:5n6)",
        "docosatrienoate (22:3n3)",
        "dodecanedioate",
        "eicosapentaenoate (EPA; 20:5n3)",
        "eicosenoate (20:1n9 or 11)",
        "ergothioneine",
        "erucate (22:1n9)",
        "erythritol",
        "erythronate*",
        "ethanolamine",
        "flavin adenine dinucleotide (FAD)",
        "fructose",
        "fructose 1-phosphate",
        "fructose-6-phosphate",
        "fucose",
        "fumarate",
        "gabapentin",
        "galactose",
        "gamma-aminobutyrate (GABA)",
        "gamma-glutamylcysteine",
        "gamma-glutamylglutamate",
        "gamma-glutamylglutamine",
        "gamma-glutamylisoleucine*",
        "gamma-glutamylleucine",
        "gamma-glutamylphenylalanine",
        "gamma-glutamylvaline",
        "gamma-tocopherol",
        "glucarate (saccharate)",
        "gluconate",
        "glucose",
        "glucose 1-phosphate",
        "glucose-6-phosphate (G6P)",
        "glucuronate",
        "glutamate",
        "glutamate, gamma-methyl ester",
        "glutamine",
        "glutarate (pentanedioate)",
        "glutaroyl carnitine",
        "glutathione, oxidized (GSSG)",
        "glutathione, reduced (GSH)",
        "glycerate",
        "glycerol",
        "glycerol 2-phosphate",
        "glycerol 3-phosphate (G3P)",
        "glycerophosphoethanolamine",
        "glycerophosphorylcholine (GPC)",
        "glycine",
        "glycocholenate sulfate*",
        "glycolate (hydroxyacetate)",
        "glycolithocholate sulfate*",
        "glycylglycine",
        "glycylisoleucine",
        "glycylleucine",
        "glycyllysine",
        "glycylmethionine",
        "glycylphenylalanine",
        "glycylproline",
        "glycylthreonine",
        "glycyltryptophan",
        "glycyltyrosine",
        "glycylvaline",
        "guanidinoacetate",
        "guanine",
        "guanosine",
        "guanosine 5'- monophosphate (5'-GMP)",
        "gulono-1,4-lactone",
        "heme",
        "hexanoylcarnitine",
        "hippurate",
        "histamine",
        "histidine",
        "histidylleucine",
        "histidylmethionine",
        "histidylphenylalanine",
        "histidyltryptophan",
        "histidyltyrosine",
        "homocysteine",
        "homoserine",
        "homostachydrine*",
        "hydrochlorothiazide",
        "hypotaurine",
        "hypoxanthine",
        "imidazole propionate",
        "indoleacetate",
        "indolelactate",
        "inosine",
        "inositol 1-phosphate (I1P)",
        "Isobar: fructose 1,6-diphosphate, glucose 1,6-diphosphate, myo-inositol 1,4 or 1,3-diphosphate",
        "Isobar: ribulose 5-phosphate, xylulose 5-phosphate",
        "isobutyrylcarnitine",
        "isoleucine",
        "isoleucylalanine",
        "isoleucylarginine",
        "isoleucylglutamate",
        "isoleucylglycine",
        "isoleucylhistidine",
        "isoleucylisoleucine",
        "isoleucylmethionine",
        "isoleucylphenylalanine",
        "isoleucylserine",
        "isoleucyltryptophan",
        "isoleucyltyrosine",
        "isoleucylvaline",
        "isovalerylcarnitine",
        "kynurenine",
        "lactate",
        "laurate (12:0)",
        "laurylcarnitine",
        "leucine",
        "leucylalanine",
        "leucylarginine",
        "leucylasparagine",
        "leucylglutamate",
        "leucylglycine",
        "leucylhistidine",
        "leucylleucine",
        "leucylmethionine",
        "leucylphenylalanine",
        "leucylserine",
        "leucyltryptophan",
        "leucyltyrosine",
        "lidocaine",
        "linoleate (18:2n6)",
        "linolenate [alpha or gamma; (18:3n3 or 6)]",
        "L-urobilin",
        "lysine",
        "lysylleucine",
        "lysyllysine",
        "lysylmethionine",
        "lysyltyrosine",
        "malate",
        "malonylcarnitine",
        "maltohexaose",
        "maltopentaose",
        "maltose",
        "maltotetraose",
        "maltotriose",
        "mannitol",
        "mannose",
        "mannose-6-phosphate",
        "margarate (17:0)",
        "metformin",
        "methionine",
        "methionylalanine",
        "methionylasparagine",
        "methionylaspartate",
        "methionylglutamate",
        "methionylglycine",
        "methionylleucine",
        "methionylphenylalanine",
        "methyl-alpha-glucopyranoside",
        "methylglutaroylcarnitine",
        "methylphosphate",
        "metoprolol",
        "metoprolol acid metabolite*",
        "myo-inositol",
        "myristate (14:0)",
        "myristoleate (14:1n5)",
        "myristoylcarnitine",
        "N1-Methyl-2-pyridone-5-carboxamide",
        "N1-methyladenosine",
        "N1-methylguanosine",
        "N2,N2-dimethylguanosine",
        "N2-acetyllysine",
        "N2-methylguanosine",
        "N6-acetyllysine",
        "N6-carbamoylthreonyladenosine",
        "N-6-trimethyllysine",
        "N-acetylalanine",
        "N-acetylarginine",
        "N-acetylasparagine",
        "N-acetylaspartate (NAA)",
        "N-acetyl-aspartyl-glutamate (NAAG)",
        "N-acetylglucosamine",
        "N-acetylglucosamine 6-phosphate",
        "N-acetylglutamine",
        "N-acetylglycine",
        "N-acetylisoleucine",
        "N-acetylleucine",
        "N-acetylmethionine",
        "N-acetylneuraminate",
        "N-acetylornithine",
        "N-acetylphenylalanine",
        "N-acetylserine",
        "N-acetylthreonine",
        "N-acetyltryptophan",
        "N-acetyltyrosine",
        "N-acetylvaline",
        "nervonate (24:1n9)",
        "nicotinamide",
        "nicotinamide adenine dinucleotide (NAD+)",
        "nicotinamide adenine dinucleotide reduced (NADH)",
        "nicotinamide ribonucleotide (NMN)",
        "nicotinamide riboside*",
        "nicotinate",
        "N-methylglutamate",
        "octanoylcarnitine",
        "oleate (18:1n9)",
        "oleoylcarnitine",
        "ophthalmate",
        "ornithine",
        "p-acetamidophenylglucuronide",
        "palmitate (16:0)",
        "palmitoleate (16:1n7)",
        "palmitoyl sphingomyelin",
        "palmitoylcarnitine",
        "pantothenate",
        "paroxetine",
        "p-cresol sulfate",
        "pelargonate (9:0)",
        "penicillin G",
        "pentadecanoate (15:0)",
        "phenol red",
        "phenol sulfate",
        "phenylacetylglutamine",
        "phenylalanine",
        "phenylalanylalanine",
        "phenylalanylarginine",
        "phenylalanylaspartate",
        "phenylalanylglutamate",
        "phenylalanylglycine",
        "phenylalanylleucine",
        "phenylalanylmethionine",
        "phenylalanylphenylalanine",
        "phenylalanylproline",
        "phenylalanylserine",
        "phenylalanyltryptophan",
        "phenylalanyltyrosine",
        "phenylalanylvaline",
        "phosphate",
        "phosphoenolpyruvate (PEP)",
        "phosphoethanolamine",
        "phytosphingosine",
        "pipecolate",
        "piperine",
        "pivaloylcarnitine",
        "pregnanediol-3-glucuronide",
        "pregnen-diol disulfate*",
        "pro-hydroxy-pro",
        "proline",
        "prolylglycine",
        "prolylmethionine",
        "propionylcarnitine",
        "prostaglandin A2",
        "prostaglandin E2",
        "pseudouridine",
        "putrescine",
        "pyridoxal",
        "pyridoxate",
        "pyroglutamine*",
        "pyrophosphate (PPi)",
        "quebrachitol",
        "quinate",
        "quinidine",
        "quinolinate",
        "ranitidine",
        "ribitol",
        "riboflavin (Vitamin B2)",
        "ribose",
        "ribulose",
        "saccharopine",
        "S-adenosylhomocysteine (SAH)",
        "S-adenosylmethionine (SAM)",
        "sarcosine (N-Methylglycine)",
        "scyllo-inositol",
        "sedoheptulose-7-phosphate",
        "serine",
        "serylisoleucine*",
        "serylleucine",
        "serylphenyalanine",
        "serylvaline",
        "S-methylcysteine",
        "sorbitol",
        "sorbitol 6-phosphate",
        "spermidine",
        "spermine",
        "sphinganine",
        "sphingosine",
        "squalene",
        "stachydrine",
        "stearate (18:0)",
        "stearidonate (18:4n3)",
        "stearoylcarnitine",
        "streptomycin",
        "succinate",
        "succinylcarnitine",
        "tartarate",
        "taurine",
        "testosterone",
        "theobromine",
        "threitol",
        "threonate",
        "threonine",
        "threonylglutamate",
        "threonylleucine",
        "threonylmethionine",
        "threonylphenylalanine",
        "threonylvaline",
        "thymidine",
        "thymine",
        "trans-4-hydroxyproline",
        "trans-urocanate",
        "triethyleneglycol",
        "trigonelline (N'-methylnicotinate)",
        "tryptophan",
        "tryptophan betaine",
        "tryptophylasparagine",
        "tryptophylglutamate",
        "tryptophylleucine",
        "tyrosine",
        "tyrosylalanine",
        "tyrosylglutamine",
        "tyrosylglycine",
        "tyrosylhistidine",
        "tyrosylleucine",
        "tyrosyllysine",
        "tyrosylphenylalanine",
        "tyrosyltyrosine",
        "tyrosylvaline",
        "undecanedioate",
        "uracil",
        "urate",
        "urea",
        "uridine",
        "uridine monophosphate (5' or 3')",
        "valerylcarnitine",
        "valine",
        "valylalanine",
        "valylarginine",
        "valylasparagine",
        "valylaspartate",
        "valylglutamate",
        "valylglutamine",
        "valylglycine",
        "valylhistidine",
        "valylisoleucine",
        "valylleucine",
        "valyllysine",
        "valylmethionine",
        "valylphenylalanine",
        "valylserine",
        "valyltryptophan",
        "valyltyrosine",
        "valylvaline",
        "vanillylmandelate (VMA)",
        "venlafaxine",
        "VGAHAGEYGAEALER*",
        "xanthine",
        "xanthosine",
        "xylitol",
        "xylonate",
        "xylose",
        "xylulose"
      ],
      "rows": 276,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_norm_se",
      "title": "tissue_norm_se",
      "object": "tissue_norm_se",
      "file": "tissue_norm_se.rda",
      "class": [
        "SummarizedExperiment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "tissue_tvn_proteomics",
      "title": "tissue_tvn_proteomics",
      "object": "tissue_tvn_proteomics",
      "file": "tissue_tvn_proteomics.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "gene_name",
        "entrezgene_id",
        "Log2FC",
        "p.val",
        "p.adj",
        "t.val",
        "SiRCleCluster_RG2",
        "SiRCleThreshold_DNA-Methylation",
        "SiRCleThreshold_RNA",
        "SiRCleThreshold_Protein"
      ],
      "rows": 8769,
      "table": true,
      "tojson": true
    },
    {
      "name": "tissue_tvn_rnaseq",
      "title": "tissue_tvn_rnaseq",
      "object": "tissue_tvn_rnaseq",
      "file": "tissue_tvn_rnaseq.rda",
      "class": [
        "spec_tbl_df",
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "gene_name",
        "entrezgene_id",
        "Log2FC",
        "p.val",
        "p.adj",
        "t.val",
        "SiRCleCluster_RG2",
        "SiRCleThreshold_DNA-Methylation",
        "SiRCleThreshold_RNA",
        "SiRCleThreshold_Protein"
      ],
      "rows": 29283,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "alanine_pathways",
      "title": "alanine_pathways",
      "topics": [
        "alanine_pathways"
      ]
    },
    {
      "page": "biocrates_features",
      "title": "biocrates_features",
      "topics": [
        "biocrates_features"
      ]
    },
    {
      "page": "cellular_meta",
      "title": "cellular_meta",
      "topics": [
        "cellular_meta"
      ]
    },
    {
      "page": "checkmatch_pk_to_data",
      "title": "Check and summarize relationship between prixor knowledge to measured",
      "topics": [
        "checkmatch_pk_to_data"
      ]
    },
    {
      "page": "cluster_ora",
      "title": "Overrepresentation analysis by cluster",
      "topics": [
        "cluster_ora"
      ]
    },
    {
      "page": "cluster_pk",
      "title": "Cluster terms in prior knowledge by set overlap",
      "topics": [
        "cluster_pk"
      ]
    },
    {
      "page": "compare_pk",
      "title": "Compare Prior Knowledge Resources and/or Columns within a Single Resource",
      "topics": [
        "compare_pk"
      ]
    },
    {
      "page": "count_id",
      "title": "Count Entries and Generate a Histogram Plot for a Specified Column",
      "topics": [
        "count_id"
      ]
    },
    {
      "page": "dma",
      "title": "Differential metabolite analysis",
      "topics": [
        "dma"
      ]
    },
    {
      "page": "equivalent_features",
      "title": "equivalent_features",
      "topics": [
        "equivalent_features"
      ]
    },
    {
      "page": "equivalent_id",
      "title": "Find additional potential IDs for \"kegg\", \"pubchem\", \"chebi\", \"hmdb\"",
      "topics": [
        "equivalent_id"
      ]
    },
    {
      "page": "gaude_pathways",
      "title": "gaude_pathways",
      "topics": [
        "gaude_pathways"
      ]
    },
    {
      "page": "get_exclusion_metabolites",
      "title": "Metabolites excluded from prior knowledge resources",
      "topics": [
        "get_exclusion_metabolites"
      ]
    },
    {
      "page": "hallmarks",
      "title": "hallmarks",
      "topics": [
        "hallmarks"
      ]
    },
    {
      "page": "intracell_dma",
      "title": "intracell_dma",
      "topics": [
        "intracell_dma"
      ]
    },
    {
      "page": "intracell_raw",
      "title": "intracell_raw",
      "topics": [
        "intracell_raw"
      ]
    },
    {
      "page": "intracell_raw_se",
      "title": "intracell_raw_se",
      "topics": [
        "intracell_raw_se"
      ]
    },
    {
      "page": "make_gene_metab_set",
      "title": "Create metabolite sets from existing genesets",
      "topics": [
        "make_gene_metab_set"
      ]
    },
    {
      "page": "mapping_ambiguity",
      "title": "Create Mapping Ambiguities between two ID types",
      "topics": [
        "mapping_ambiguity"
      ]
    },
    {
      "page": "mca_2cond",
      "title": "Metabolite clustering analysis for two conditions",
      "topics": [
        "mca_2cond"
      ]
    },
    {
      "page": "mca_core",
      "title": "Metabolite clustering analysis for core experiments",
      "topics": [
        "mca_core"
      ]
    },
    {
      "page": "mca_core_rules",
      "title": "mca_core_rules",
      "topics": [
        "mca_core_rules"
      ]
    },
    {
      "page": "mca_twocond_rules",
      "title": "mca_twocond_rules",
      "topics": [
        "mca_twocond_rules"
      ]
    },
    {
      "page": "medium_raw",
      "title": "medium_raw",
      "topics": [
        "medium_raw"
      ]
    },
    {
      "page": "meta_pk",
      "title": "Meta prior-knowledge",
      "topics": [
        "meta_pk"
      ]
    },
    {
      "page": "metadata_analysis",
      "title": "PCA-based metadata analysis",
      "topics": [
        "metadata_analysis"
      ]
    },
    {
      "page": "MetaProViz",
      "title": "The MetaProViz package",
      "topics": [
        "MetaProViz-package",
        "MetaProViz"
      ]
    },
    {
      "page": "metaproviz_config_path",
      "title": "Current config file path of MetaProViz",
      "topics": [
        "metaproviz_config_path"
      ]
    },
    {
      "page": "metaproviz_load_config",
      "title": "Load the package configuration from a config file",
      "topics": [
        "metaproviz_load_config"
      ]
    },
    {
      "page": "metaproviz_log",
      "title": "Browse the current MetaProViz log file",
      "topics": [
        "metaproviz_log"
      ]
    },
    {
      "page": "metaproviz_logfile",
      "title": "Path to the current MetaProViz log file",
      "topics": [
        "metaproviz_logfile"
      ]
    },
    {
      "page": "metaproviz_reset_config",
      "title": "Restore the built-in default values of all config parameters of MetaProViz",
      "topics": [
        "metaproviz_reset_config"
      ]
    },
    {
      "page": "metaproviz_save_config",
      "title": "Save the current package configuration",
      "topics": [
        "metaproviz_save_config"
      ]
    },
    {
      "page": "metaproviz_set_loglevel",
      "title": "Sets the log level for the package logger",
      "topics": [
        "metaproviz_set_loglevel"
      ]
    },
    {
      "page": "metsigdb_chemicalclass",
      "title": "Metabolite chemical classes from RaMP DB",
      "topics": [
        "metsigdb_chemicalclass"
      ]
    },
    {
      "page": "metsigdb_kegg",
      "title": "KEGG pathways",
      "topics": [
        "metsigdb_kegg"
      ]
    },
    {
      "page": "metsigdb_macdb",
      "title": "Retrieve MACDB metabolite-cancer associations.",
      "topics": [
        "metsigdb_macdb"
      ]
    },
    {
      "page": "metsigdb_metalinks",
      "title": "Annotated metabolite-protein interactions from MetalinksDB",
      "topics": [
        "metsigdb_metalinks"
      ]
    },
    {
      "page": "metsigdb_reactome",
      "title": "Retrieve Reactome metabolite sets suitable for ORA.",
      "topics": [
        "metsigdb_reactome"
      ]
    },
    {
      "page": "metsigdb_wikipathways",
      "title": "Retrieve WikiPathways metabolite mapping suitable for ORA.",
      "topics": [
        "metsigdb_wikipathways"
      ]
    },
    {
      "page": "pool_estimation",
      "title": "Find metabolites with high variability across total pool samples",
      "topics": [
        "pool_estimation"
      ]
    },
    {
      "page": "processing",
      "title": "Data preprocessing and normalization",
      "topics": [
        "processing"
      ]
    },
    {
      "page": "replicate_sum",
      "title": "Merges the analytical replicates of an experiment",
      "topics": [
        "replicate_sum"
      ]
    },
    {
      "page": "standard_ora",
      "title": "Overrepresentation analysis of metabolite sets in pathways",
      "topics": [
        "standard_ora"
      ]
    },
    {
      "page": "tissue_dma",
      "title": "tissue_dma",
      "topics": [
        "tissue_dma"
      ]
    },
    {
      "page": "tissue_dma_old",
      "title": "tissue_dma_old",
      "topics": [
        "tissue_dma_old"
      ]
    },
    {
      "page": "tissue_dma_young",
      "title": "tissue_dma_young",
      "topics": [
        "tissue_dma_young"
      ]
    },
    {
      "page": "tissue_meta",
      "title": "Tissue_Metadata",
      "topics": [
        "tissue_meta"
      ]
    },
    {
      "page": "tissue_norm",
      "title": "tissue_norm",
      "topics": [
        "tissue_norm"
      ]
    },
    {
      "page": "tissue_norm_se",
      "title": "tissue_norm_se",
      "topics": [
        "tissue_norm_se"
      ]
    },
    {
      "page": "tissue_tvn_proteomics",
      "title": "tissue_tvn_proteomics",
      "topics": [
        "tissue_tvn_proteomics"
      ]
    },
    {
      "page": "tissue_tvn_rnaseq",
      "title": "tissue_tvn_rnaseq",
      "topics": [
        "tissue_tvn_rnaseq"
      ]
    },
    {
      "page": "translate_id",
      "title": "Translate IDs to/from KEGG, PubChem, Chebi, HMDB",
      "topics": [
        "translate_id"
      ]
    },
    {
      "page": "traverse_ids",
      "title": "Expand metabolite IDs by traversing RaMP ID mappings",
      "topics": [
        "traverse_ids"
      ]
    },
    {
      "page": "viz_graph",
      "title": "Graph visualization for clustered terms",
      "topics": [
        "viz_graph"
      ]
    },
    {
      "page": "viz_heatmap",
      "title": "Heatmap visualization",
      "topics": [
        "viz_heatmap"
      ]
    },
    {
      "page": "viz_pca",
      "title": "This script allows you to perform PCA plot visualization using the results of the MetaProViz analysis",
      "topics": [
        "viz_pca"
      ]
    },
    {
      "page": "viz_superplot",
      "title": "This script allows you to perform different visualizations (bar, box, violin plots) using the results of the MetaProViz analysis",
      "topics": [
        "viz_superplot"
      ]
    },
    {
      "page": "viz_volcano",
      "title": "Volcano plot",
      "topics": [
        "viz_volcano"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/MetaProViz/raw/HEAD/README.md",
  "_rundeps": [
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    "backports",
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    "BH",
    "Biobase",
    "BiocGenerics",
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    "Biostrings",
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    "bit64",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "CARNIVAL",
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    "checkmate",
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    "cluster",
    "codetools",
    "colorspace",
    "ComplexUpset",
    "corrplot",
    "cosmosR",
    "cowplot",
    "cpp11",
    "crayon",
    "crosstalk",
    "curl",
    "DBI",
    "decoupleR",
    "DelayedArray",
    "dendextend",
    "Deriv",
    "digest",
    "doBy",
    "dorothea",
    "dplyr",
    "DT",
    "ellipse",
    "emmeans",
    "EnhancedVolcano",
    "estimability",
    "evaluate",
    "factoextra",
    "FactoMineR",
    "farver",
    "fastmap",
    "flashClust",
    "fontawesome",
    "forecast",
    "formatR",
    "Formula",
    "fracdiff",
    "fs",
    "futile.logger",
    "futile.options",
    "generics",
    "GenomicRanges",
    "ggbeeswarm",
    "ggforce",
    "ggfortify",
    "ggplot2",
    "ggpubr",
    "ggraph",
    "ggrepel",
    "ggsci",
    "ggsignif",
    "glue",
    "graph",
    "graphlayouts",
    "gridExtra",
    "GSEABase",
    "gtable",
    "gtools",
    "hash",
    "highr",
    "hms",
    "htmltools",
    "htmlwidgets",
    "httr",
    "httr2",
    "igraph",
    "inflection",
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    "lubridate",
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    "Matrix",
    "MatrixGenerics",
    "MatrixModels",
    "matrixStats",
    "memoise",
    "mgcv",
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    "mime",
    "minqa",
    "modelr",
    "multcompView",
    "mvtnorm",
    "nlme",
    "nloptr",
    "nnet",
    "numDeriv",
    "OmnipathR",
    "openssl",
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    "pheatmap",
    "pillar",
    "pkgconfig",
    "plyr",
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    "Polychrome",
    "polyclip",
    "polynom",
    "prettyunits",
    "progress",
    "promises",
    "purrr",
    "qcc",
    "quantreg",
    "qvalue",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "rbibutils",
    "RColorBrewer",
    "Rcpp",
    "RcppArmadillo",
    "RcppEigen",
    "Rdpack",
    "readr",
    "readxl",
    "reformulas",
    "rematch",
    "reshape2",
    "rjson",
    "rlang",
    "rmarkdown",
    "RSQLite",
    "rstatix",
    "rvest",
    "S4Arrays",
    "S4Vectors",
    "S7",
    "sass",
    "scales",
    "scatterplot3d",
    "selectr",
    "Seqinfo",
    "sessioninfo",
    "snow",
    "SparseArray",
    "SparseM",
    "statmod",
    "stringi",
    "stringr",
    "SummarizedExperiment",
    "survival",
    "sys",
    "systemfonts",
    "tibble",
    "tidygraph",
    "tidyr",
    "tidyselect",
    "timechange",
    "timeDate",
    "tinytex",
    "tweenr",
    "tzdb",
    "urca",
    "utf8",
    "vctrs",
    "vipor",
    "viridis",
    "viridisLite",
    "visNetwork",
    "vroom",
    "withr",
    "writexl",
    "xfun",
    "XML",
    "xml2",
    "xtable",
    "XVector",
    "yaml",
    "zip",
    "zoo"
  ],
  "_vignettes": [
    {
      "source": "quick-start.Rmd",
      "filename": "quick-start.html",
      "title": "Getting started with MetaProViz",
      "author": "Christina Schmidt",
      "engine": "knitr::rmarkdown",
      "headings": [
        "1. Loading the example data",
        "2. Pre-processing",
        "PCA plot and Heatmap",
        "3. Differential Metabolite Analysis",
        "Volcano Plots",
        "3. Enrichment Analysis and Prior knowledge",
        "Match IDs with PK",
        "Run ORA",
        "Volcano plot",
        "4. Metabolite Clustering Analysis",
        "MCA-2Cond",
        "MCA-CoRe",
        "ORA on each metabolite cluster",
        "Viz",
        "Session information",
        "Bibliography"
      ],
      "created": "2025-10-07 21:39:30",
      "modified": "2026-03-23 15:02:21",
      "commits": 8
    }
  ],
  "_score": 7.440909082065218,
  "_indexed": true,
  "_nocasepkg": "metaproviz",
  "_universes": [
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    "saezlab"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "4.1.0",
      "date": "2026-05-30T10:10:42.000Z",
      "distro": "noble",
      "commit": "02799d0d5ac3648b123862d0baf76f31f72b2441",
      "fileid": "546b9b2136eddef057b9af4c12d61a7ac06f2d7fb06253de1f72d38c919d3e1b",
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