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        "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": [],
      "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/RELEASE_3_23/README.md",
  "_rundeps": [
    "abind",
    "annotate",
    "AnnotationDbi",
    "askpass",
    "backports",
    "base64enc",
    "bcellViper",
    "beeswarm",
    "BH",
    "Biobase",
    "BiocGenerics",
    "BiocParallel",
    "Biostrings",
    "bit",
    "bit64",
    "blob",
    "boot",
    "broom",
    "bslib",
    "cachem",
    "car",
    "carData",
    "CARNIVAL",
    "cellranger",
    "checkmate",
    "cli",
    "clipr",
    "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",
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