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  "Description": "Lipid annotation in untargeted LC-MS lipidomics based on\nfragmentation rules. Alcoriza-Balaguer MI, Garcia-Canaveras JC,\nLopez A, Conde I, Juan O, Carretero J, Lahoz A (2019)\n<doi:10.1021/acs.analchem.8b03409>.",
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    "idSMneg",
    "idSMpos",
    "idSphneg",
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    "idSphpos",
    "idSphPpos",
    "idTGpos",
    "LipidMSapp",
    "organizeResults",
    "ploteicmsbatch",
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    "plotticmsbatch",
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    "searchIsotopes",
    "searchIsotopesmsbatch",
    "setmsbatch"
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      "title": "PEs database",
      "object": "pedb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 147,
      "table": true,
      "tojson": true
    },
    {
      "name": "peodb",
      "title": "O-PE database",
      "object": "peodb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 46,
      "table": true,
      "tojson": true
    },
    {
      "name": "pepdb",
      "title": "P-PE database",
      "object": "pepdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 38,
      "table": true,
      "tojson": true
    },
    {
      "name": "pgdb",
      "title": "PGs database",
      "object": "pgdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 147,
      "table": true,
      "tojson": true
    },
    {
      "name": "pidb",
      "title": "PIs database",
      "object": "pidb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 147,
      "table": true,
      "tojson": true
    },
    {
      "name": "psdb",
      "title": "PSs database",
      "object": "psdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 147,
      "table": true,
      "tojson": true
    },
    {
      "name": "smdb",
      "title": "SMs database",
      "object": "smdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 52,
      "table": true,
      "tojson": true
    },
    {
      "name": "sphdb",
      "title": "Sphingoid bases database",
      "object": "sphdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "sphPdb",
      "title": "Sphingoid bases phosphate database",
      "object": "sphPdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 4,
      "table": true,
      "tojson": true
    },
    {
      "name": "tgdb",
      "title": "TGs database",
      "object": "tgdb",
      "class": [
        "data.frame"
      ],
      "fields": [
        "formula",
        "total",
        "Mass"
      ],
      "rows": 376,
      "table": true,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "acylcerdb",
      "title": "AcylCeramides database",
      "topics": [
        "acylcerdb"
      ]
    },
    {
      "page": "adductsTable",
      "title": "Adducts table",
      "topics": [
        "adductsTable"
      ]
    },
    {
      "page": "alignmsbatch",
      "title": "Align samples from an msbatch",
      "topics": [
        "alignmsbatch"
      ]
    },
    {
      "page": "annotatemsbatch",
      "title": "Lipid annotation for an msbatch",
      "topics": [
        "annotatemsbatch"
      ]
    },
    {
      "page": "assignDB",
      "title": "Load LipidMS default data bases",
      "topics": [
        "assignDB"
      ]
    },
    {
      "page": "baconjdb",
      "title": "Bile acids conjugates database",
      "topics": [
        "baconjdb"
      ]
    },
    {
      "page": "badb",
      "title": "Bile acids database",
      "topics": [
        "badb"
      ]
    },
    {
      "page": "batchdataProcessing",
      "title": "Process several mzXML files (peakpicking and isotope annotation) and create an msbatch for batch processing.",
      "topics": [
        "batchdataProcessing"
      ]
    },
    {
      "page": "carnitinedb",
      "title": "Carnitine database",
      "topics": [
        "carnitinedb"
      ]
    },
    {
      "page": "CEdb",
      "title": "CEs database",
      "topics": [
        "CEdb"
      ]
    },
    {
      "page": "cerdb",
      "title": "Ceramides database",
      "topics": [
        "cerdb"
      ]
    },
    {
      "page": "cerPdb",
      "title": "Ceramides Phosphate database",
      "topics": [
        "cerPdb"
      ]
    },
    {
      "page": "chainFrags",
      "title": "Search of chain specific fragments",
      "topics": [
        "chainFrags"
      ]
    },
    {
      "page": "checkClass",
      "title": "Search of class fragments to confirm the lipid class.",
      "topics": [
        "checkClass"
      ]
    },
    {
      "page": "checkIntensityRules",
      "title": "Check intensity rules",
      "topics": [
        "checkIntensityRules"
      ]
    },
    {
      "page": "cldb",
      "title": "Cardiolipins database",
      "topics": [
        "cldb"
      ]
    },
    {
      "page": "coelutingFrags",
      "title": "Coeluting fragments extraction",
      "topics": [
        "coelutingFrags"
      ]
    },
    {
      "page": "coelutionScore",
      "title": "calculate coelution score between two peaks",
      "topics": [
        "coelutionScore"
      ]
    },
    {
      "page": "combineChains",
      "title": "Combine chain fragments that could belong to the same precursor.",
      "topics": [
        "combineChains"
      ]
    },
    {
      "page": "confLevels",
      "title": "Confidence Annotation Levels",
      "topics": [
        "confLevels"
      ]
    },
    {
      "page": "createLipidDB",
      "title": "Customizable lipid DBs creator",
      "topics": [
        "createLipidDB"
      ]
    },
    {
      "page": "crossTables",
      "title": "Cross the original MS1 peaklist with the annotation results",
      "topics": [
        "crossTables"
      ]
    },
    {
      "page": "dataProcessing",
      "title": "Process mzXML files individually: peakpicking and isotope annotation",
      "topics": [
        "dataProcessing"
      ]
    },
    {
      "page": "ddaFrags",
      "title": "MS/MS scan extraction of a precursor in DDA",
      "topics": [
        "ddaFrags"
      ]
    },
    {
      "page": "dgdb",
      "title": "DGs database",
      "topics": [
        "dgdb"
      ]
    },
    {
      "page": "fadb",
      "title": "FAs database",
      "topics": [
        "fadb"
      ]
    },
    {
      "page": "fahfadb",
      "title": "FAHFAs database",
      "topics": [
        "fahfadb"
      ]
    },
    {
      "page": "fillpeaksmsbatch",
      "title": "Fill peaks from a grouped msbatch",
      "topics": [
        "fillpeaksmsbatch"
      ]
    },
    {
      "page": "findCandidates",
      "title": "Search of lipid candidates of a certain class",
      "topics": [
        "findCandidates"
      ]
    },
    {
      "page": "getInclusionList",
      "title": "Obtain an inclusion list from the annotation results",
      "topics": [
        "getInclusionList"
      ]
    },
    {
      "page": "groupmsbatch",
      "title": "Group features from an msbatch",
      "topics": [
        "groupmsbatch"
      ]
    },
    {
      "page": "hfadb",
      "title": "HFAs database",
      "topics": [
        "hfadb"
      ]
    },
    {
      "page": "idAcylCerneg",
      "title": "Acylceramides (AcylCer) annotation for ESI-",
      "topics": [
        "idAcylCerneg"
      ]
    },
    {
      "page": "idAcylCerpos",
      "title": "Acylceramides (AcylCer) annotation for ESI+",
      "topics": [
        "idAcylCerpos"
      ]
    },
    {
      "page": "idBAneg",
      "title": "Bile Acids (BA) annotation for ESI-",
      "topics": [
        "idBAneg"
      ]
    },
    {
      "page": "idCarpos",
      "title": "Acylcarnitine annotation for ESI+",
      "topics": [
        "idCarpos"
      ]
    },
    {
      "page": "idCEpos",
      "title": "Cholesteryl Esters (CE) annotation for ESI+",
      "topics": [
        "idCEpos"
      ]
    },
    {
      "page": "idCerneg",
      "title": "Ceramides (Cer) annotation for ESI-",
      "topics": [
        "idCerneg"
      ]
    },
    {
      "page": "idCerPneg",
      "title": "Ceramides phosphate (CerP) annotation for ESI-",
      "topics": [
        "idCerPneg"
      ]
    },
    {
      "page": "idCerpos",
      "title": "Ceramides (Cer) annotation for ESI+",
      "topics": [
        "idCerpos"
      ]
    },
    {
      "page": "idCerPpos",
      "title": "Ceramides phosphate (CerP) annotation for ESI+",
      "topics": [
        "idCerPpos"
      ]
    },
    {
      "page": "idCLneg",
      "title": "Cardiolipines (CL) annotation for ESI-",
      "topics": [
        "idCLneg"
      ]
    },
    {
      "page": "idDGpos",
      "title": "Diacylglycerols (DG) annotation for ESI+",
      "topics": [
        "idDGpos"
      ]
    },
    {
      "page": "idFAHFAneg",
      "title": "FAHFA annotation for ESI-",
      "topics": [
        "idFAHFAneg"
      ]
    },
    {
      "page": "idFAneg",
      "title": "Fatty Acids (FA) annotation for ESI-",
      "topics": [
        "idFAneg"
      ]
    },
    {
      "page": "idLPCneg",
      "title": "Lysophosphocholines (LPC) annotation for ESI-",
      "topics": [
        "idLPCneg"
      ]
    },
    {
      "page": "idLPCpos",
      "title": "Lysophosphocholines (LPC) annotation for ESI+",
      "topics": [
        "idLPCpos"
      ]
    },
    {
      "page": "idLPEneg",
      "title": "Lysophosphoethanolamines (LPE) annotation for ESI-",
      "topics": [
        "idLPEneg"
      ]
    },
    {
      "page": "idLPEpos",
      "title": "Lysophosphoethanolamines (LPE) annotation for ESI+",
      "topics": [
        "idLPEpos"
      ]
    },
    {
      "page": "idLPGneg",
      "title": "Lysophosphoglycerols (LPG) annotation for ESI-",
      "topics": [
        "idLPGneg"
      ]
    },
    {
      "page": "idLPIneg",
      "title": "Lysophosphoinositols (LPI) annotation for ESI-",
      "topics": [
        "idLPIneg"
      ]
    },
    {
      "page": "idLPSneg",
      "title": "Lysophosphoserines (LPS) annotation for ESI-",
      "topics": [
        "idLPSneg"
      ]
    },
    {
      "page": "idMGpos",
      "title": "Monoacylglycerol (MG) annotation for ESI+",
      "topics": [
        "idMGpos"
      ]
    },
    {
      "page": "idNEG",
      "title": "Lipids annotation for ESI-",
      "topics": [
        "idNEG"
      ]
    },
    {
      "page": "idPCneg",
      "title": "Phosphocholines (PC) annotation for ESI-",
      "topics": [
        "idPCneg"
      ]
    },
    {
      "page": "idPConeg",
      "title": "Plasmanyl Phosphocholines (PCo) annotation for ESI-",
      "topics": [
        "idPConeg"
      ]
    },
    {
      "page": "idPCopos",
      "title": "Plasmanyl Phosphocholines (PCo) annotation for ESI+",
      "topics": [
        "idPCopos"
      ]
    },
    {
      "page": "idPCpneg",
      "title": "Plasmenyl Phosphocholines (PCp) annotation for ESI-",
      "topics": [
        "idPCpneg"
      ]
    },
    {
      "page": "idPCpos",
      "title": "Phosphocholines (PC) annotation for ESI+",
      "topics": [
        "idPCpos"
      ]
    },
    {
      "page": "idPCppos",
      "title": "Plasmenyl Phosphocholines (PCp) annotation for ESI+",
      "topics": [
        "idPCppos"
      ]
    },
    {
      "page": "idPEneg",
      "title": "Phosphoethanolamines (PE) annotation for ESI-",
      "topics": [
        "idPEneg"
      ]
    },
    {
      "page": "idPEoneg",
      "title": "Plasmanyl Phosphoethanolamines (PEo) annotation for ESI-",
      "topics": [
        "idPEoneg"
      ]
    },
    {
      "page": "idPEopos",
      "title": "Plasmanyl Phosphoethanolamines (PEo) annotation for ESI+",
      "topics": [
        "idPEopos"
      ]
    },
    {
      "page": "idPEpneg",
      "title": "Plasmenyl Phosphoethanolamines (PEp) annotation for ESI-",
      "topics": [
        "idPEpneg"
      ]
    },
    {
      "page": "idPEpos",
      "title": "Phosphoethanolamines (PE) annotation for ESI+",
      "topics": [
        "idPEpos"
      ]
    },
    {
      "page": "idPEppos",
      "title": "Plasmenyl Phosphoethanolamines (PEp) annotation for ESI+",
      "topics": [
        "idPEppos"
      ]
    },
    {
      "page": "idPGneg",
      "title": "Phosphoglycerols (PG) annotation for ESI-",
      "topics": [
        "idPGneg"
      ]
    },
    {
      "page": "idPGpos",
      "title": "Phosphoglycerols (PG) annotation for ESI+",
      "topics": [
        "idPGpos"
      ]
    },
    {
      "page": "idPIneg",
      "title": "Phosphoinositols (PI) annotation for ESI-",
      "topics": [
        "idPIneg"
      ]
    },
    {
      "page": "idPIpos",
      "title": "Phosphoinositols (PI) annotation for ESI+",
      "topics": [
        "idPIpos"
      ]
    },
    {
      "page": "idPOS",
      "title": "Lipids annotation for ESI+",
      "topics": [
        "idPOS"
      ]
    },
    {
      "page": "idPSneg",
      "title": "Phosphoserines (PS) annotation for ESI-",
      "topics": [
        "idPSneg"
      ]
    },
    {
      "page": "idSMneg",
      "title": "Sphingomyelines (SM) annotation for ESI-",
      "topics": [
        "idSMneg"
      ]
    },
    {
      "page": "idSMpos",
      "title": "Sphyngomyelines (SM) annotation for ESI+",
      "topics": [
        "idSMpos"
      ]
    },
    {
      "page": "idSphneg",
      "title": "Sphingoid bases (Sph) annotation for ESI-",
      "topics": [
        "idSphneg"
      ]
    },
    {
      "page": "idSphPneg",
      "title": "Sphingoid bases phosphate (SphP) annotation for ESI-",
      "topics": [
        "idSphPneg"
      ]
    },
    {
      "page": "idSphpos",
      "title": "Sphingoid bases (Sph) annotation for ESI-",
      "topics": [
        "idSphpos"
      ]
    },
    {
      "page": "idSphPpos",
      "title": "Sphingoid bases phosphate (SphP) annotation for ESI+",
      "topics": [
        "idSphPpos"
      ]
    },
    {
      "page": "idTGpos",
      "title": "Triacylglycerols (TG) annotation for ESI+",
      "topics": [
        "idTGpos"
      ]
    },
    {
      "page": "LipidMSapp",
      "title": "LipidMS shiny app",
      "topics": [
        "LipidMSapp"
      ]
    },
    {
      "page": "lysopadb",
      "title": "LPAs database",
      "topics": [
        "lysopadb"
      ]
    },
    {
      "page": "lysopaodb",
      "title": "O-LPA database",
      "topics": [
        "lysopaodb"
      ]
    },
    {
      "page": "lysopcdb",
      "title": "LPCs database",
      "topics": [
        "lysopcdb"
      ]
    },
    {
      "page": "lysopcodb",
      "title": "O-LPC database",
      "topics": [
        "lysopcodb"
      ]
    },
    {
      "page": "lysopcpdb",
      "title": "P-LPC database",
      "topics": [
        "lysopcpdb"
      ]
    },
    {
      "page": "lysopedb",
      "title": "LPEs database",
      "topics": [
        "lysopedb"
      ]
    },
    {
      "page": "lysopeodb",
      "title": "O-LPE database",
      "topics": [
        "lysopeodb"
      ]
    },
    {
      "page": "lysopepdb",
      "title": "P-LPE database",
      "topics": [
        "lysopepdb"
      ]
    },
    {
      "page": "lysopgdb",
      "title": "LPGs database",
      "topics": [
        "lysopgdb"
      ]
    },
    {
      "page": "lysopidb",
      "title": "LPIs database",
      "topics": [
        "lysopidb"
      ]
    },
    {
      "page": "lysopsdb",
      "title": "LPSs database",
      "topics": [
        "lysopsdb"
      ]
    },
    {
      "page": "mgdb",
      "title": "MGs database",
      "topics": [
        "mgdb"
      ]
    },
    {
      "page": "nlsphdb",
      "title": "Neutral losses db for sphingoid bases. It is employed by idCerneg function.",
      "topics": [
        "nlsphdb"
      ]
    },
    {
      "page": "organizeResults",
      "title": "Prepare output for LipidMS annotation functions",
      "topics": [
        "organizeResults"
      ]
    },
    {
      "page": "padb",
      "title": "PAs database",
      "topics": [
        "padb"
      ]
    },
    {
      "page": "pcdb",
      "title": "PCs database",
      "topics": [
        "pcdb"
      ]
    },
    {
      "page": "pcodb",
      "title": "O-PC database",
      "topics": [
        "pcodb"
      ]
    },
    {
      "page": "pcpdb",
      "title": "P-PC database",
      "topics": [
        "pcpdb"
      ]
    },
    {
      "page": "pedb",
      "title": "PEs database",
      "topics": [
        "pedb"
      ]
    },
    {
      "page": "peodb",
      "title": "O-PE database",
      "topics": [
        "peodb"
      ]
    },
    {
      "page": "pepdb",
      "title": "P-PE database",
      "topics": [
        "pepdb"
      ]
    },
    {
      "page": "pgdb",
      "title": "PGs database",
      "topics": [
        "pgdb"
      ]
    },
    {
      "page": "pidb",
      "title": "PIs database",
      "topics": [
        "pidb"
      ]
    },
    {
      "page": "ploteicmsbatch",
      "title": "EIC for all samples in a msbatch",
      "topics": [
        "ploteicmsbatch"
      ]
    },
    {
      "page": "plotLipids",
      "title": "Plot informative peaks for lipid annotation",
      "topics": [
        "plotLipids"
      ]
    },
    {
      "page": "plotticmsbatch",
      "title": "TIC for all samples in a msbatch",
      "topics": [
        "plotticmsbatch"
      ]
    },
    {
      "page": "psdb",
      "title": "PSs database",
      "topics": [
        "psdb"
      ]
    },
    {
      "page": "rtdevplot",
      "title": "Plot retention time deviation",
      "topics": [
        "rtdevplot"
      ]
    },
    {
      "page": "searchIsotopes",
      "title": "Targeted isotopes search",
      "topics": [
        "searchIsotopes"
      ]
    },
    {
      "page": "searchIsotopesmsbatch",
      "title": "Targeted isotopes search for msbatch",
      "topics": [
        "searchIsotopesmsbatch"
      ]
    },
    {
      "page": "setmsbatch",
      "title": "Create msbatch for batch processing.",
      "topics": [
        "setmsbatch"
      ]
    },
    {
      "page": "smdb",
      "title": "SMs database",
      "topics": [
        "smdb"
      ]
    },
    {
      "page": "sphdb",
      "title": "Sphingoid bases database",
      "topics": [
        "sphdb"
      ]
    },
    {
      "page": "sphPdb",
      "title": "Sphingoid bases phosphate database",
      "topics": [
        "sphPdb"
      ]
    },
    {
      "page": "tgdb",
      "title": "TGs database",
      "topics": [
        "tgdb"
      ]
    }
  ],
  "_readme": "https://github.com/maialba3/lipidms/raw/HEAD/README.md",
  "_rundeps": [
    "base64enc",
    "bslib",
    "cachem",
    "CHNOSZ",
    "cli",
    "codetools",
    "cpp11",
    "crosstalk",
    "digest",
    "DT",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fs",
    "future",
    "future.apply",
    "ggplot2",
    "globals",
    "glue",
    "gtable",
    "highr",
    "htmltools",
    "htmlwidgets",
    "isoband",
    "iterators",
    "jquerylib",
    "jsonlite",
    "knitr",
    "labeling",
    "later",
    "lazyeval",
    "lifecycle",
    "listenv",
    "magrittr",
    "memoise",
    "mime",
    "otel",
    "parallelly",
    "patchwork",
    "promises",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "R6",
    "rappdirs",
    "RColorBrewer",
    "Rcpp",
    "readMzXmlData",
    "rlang",
    "rmarkdown",
    "S7",
    "sass",
    "scales",
    "tinytex",
    "vctrs",
    "viridisLite",
    "withr",
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