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  "Package": "CePa",
  "Type": "Package",
  "Title": "Centrality-Based Pathway Enrichment",
  "Version": "0.8.0",
  "Date": "2021-04-20",
  "Author": "Zuguang Gu",
  "Maintainer": "Zuguang Gu <z.gu@dkfz.de>",
  "Description": "This package aims to find significant pathways through\nnetwork topology information. It has several advantages\ncompared with current pathway enrichment tools. First, pathway\nnode instead of single gene is taken as the basic unit when\nanalysing networks to meet the fact that genes must be\nconstructed into complexes to hold normal functions. Second,\nmultiple network centrality measures are applied simultaneously\nto measure importance of nodes from different aspects to make a\nfull view on the biological system. CePa extends standard\npathway enrichment methods, which include both\nover-representation analysis procedure and gene-set analysis\nprocedure. <https://doi.org/10.1093/bioinformatics/btt008>.",
  "LazyLoad": "yes",
  "URL": "https://github.com/jokergoo/CePa",
  "License": "GPL (>= 2)",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev zlib1g-dev",
  "Repository": "https://jokergoo.r-universe.dev",
  "Date/Publication": "2021-07-01 13:03:59 UTC",
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    "name": "Zuguang Gu",
    "description": "A bioinformagician"
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    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
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  "_realowner": "jokergoo",
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      "date": "2012-04-28"
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      "date": "2024-10-08"
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    "cepa.all",
    "cepa.all.parallel",
    "cepa.ora",
    "cepa.ora.all",
    "cepa.univariate",
    "cepa.univariate.all",
    "generate.pathway",
    "get.cepa",
    "p.table",
    "pathway.nodes",
    "plot.cepa",
    "plot.cepa.all",
    "plot.pathway.catalogue",
    "plotGraph",
    "plotNull",
    "print.cepa",
    "print.cepa.all",
    "print.pathway.catalogue",
    "radiality",
    "reach",
    "read.cls",
    "read.gct",
    "report",
    "sampleLabel",
    "set.pathway.catalogue",
    "spread"
  ],
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      "name": "gene.list",
      "title": "Differential gene list and background gene list",
      "object": "gene.list",
      "file": "gene.list.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "PID.db",
      "title": "pathway catalogues from Pathway Interaction Database(PID)",
      "object": "PID.db",
      "file": "PID.db.rda",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "CePa-package",
      "title": "Centrality-based pathway enrichment",
      "topics": [
        "CePa-package"
      ]
    },
    {
      "page": "cepa",
      "title": "Apply CePa algorithm on a single pathway",
      "topics": [
        "cepa"
      ]
    },
    {
      "page": "cepa.all",
      "title": "Apply CePa algorithm on a list of pathways under multiple centralities",
      "topics": [
        "cepa.all"
      ]
    },
    {
      "page": "cepa.all.parallel",
      "title": "use CePa package through parallel computing",
      "topics": [
        "cepa.all.parallel"
      ]
    },
    {
      "page": "cepa.ora",
      "title": "Apply centrality-extended ORA on a single pathway",
      "topics": [
        "cepa.ora"
      ]
    },
    {
      "page": "cepa.ora.all",
      "title": "Apply centrality-extented ORA on a list of pathways",
      "topics": [
        "cepa.ora.all"
      ]
    },
    {
      "page": "cepa.univariate",
      "title": "Apply centrality-extended GSA on a single pathway",
      "topics": [
        "cepa.univariate"
      ]
    },
    {
      "page": "cepa.univariate.all",
      "title": "Apply centrality-extented GSA on a list of pathways",
      "topics": [
        "cepa.univariate.all"
      ]
    },
    {
      "page": "gene.list",
      "title": "Differential gene list and background gene list",
      "topics": [
        "gene.list"
      ]
    },
    {
      "page": "generate.pathway",
      "title": "Generate igraph object from edge list",
      "topics": [
        "generate.pathway"
      ]
    },
    {
      "page": "get.cepa",
      "title": "get single cepa object from cepa.all object",
      "topics": [
        "get.cepa"
      ]
    },
    {
      "page": "p.table",
      "title": "Table of p-values of pathways",
      "topics": [
        "p.table"
      ]
    },
    {
      "page": "pathway.nodes",
      "title": "names of the pathway nodes",
      "topics": [
        "pathway.nodes"
      ]
    },
    {
      "page": "PID.db",
      "title": "pathway catalogues from Pathway Interaction Database(PID)",
      "topics": [
        "PID.db"
      ]
    },
    {
      "page": "plot.cepa",
      "title": "Plot the cepa object",
      "topics": [
        "plot.cepa"
      ]
    },
    {
      "page": "plot.cepa.all",
      "title": "plot the cepa.all object",
      "topics": [
        "plot.cepa.all"
      ]
    },
    {
      "page": "plot.pathway.catalogue",
      "title": "plot pathway.catalogue object",
      "topics": [
        "plot.pathway.catalogue"
      ]
    },
    {
      "page": "plotGraph",
      "title": "Plot graph for the pathway network",
      "topics": [
        "plotGraph"
      ]
    },
    {
      "page": "plotNull",
      "title": "Plot the null distribution of the pathway score",
      "topics": [
        "plotNull"
      ]
    },
    {
      "page": "print.cepa",
      "title": "  print the cepa object  ",
      "topics": [
        "print.cepa"
      ]
    },
    {
      "page": "print.cepa.all",
      "title": "print the cepa.all object",
      "topics": [
        "print.cepa.all"
      ]
    },
    {
      "page": "print.pathway.catalogue",
      "title": "print pathway.catalogue object",
      "topics": [
        "print.pathway.catalogue"
      ]
    },
    {
      "page": "radiality",
      "title": "Calculate radiality centrality",
      "topics": [
        "radiality"
      ]
    },
    {
      "page": "reach",
      "title": "Calculate largest reach centrality",
      "topics": [
        "reach"
      ]
    },
    {
      "page": "read.cls",
      "title": "Read CLS file which stores the phenotype data",
      "topics": [
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      ]
    },
    {
      "page": "read.gct",
      "title": "Read GCT format file which stores the expression values",
      "topics": [
        "read.gct"
      ]
    },
    {
      "page": "report",
      "title": "Generate report for CePa analysis",
      "topics": [
        "report"
      ]
    },
    {
      "page": "sampleLabel",
      "title": "Generate data structure of sample labels",
      "topics": [
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      ]
    },
    {
      "page": "set.pathway.catalogue",
      "title": "store pathway data and pre-processing",
      "topics": [
        "set.pathway.catalogue"
      ]
    },
    {
      "page": "spread",
      "title": "Calculate radiality centrality",
      "topics": [
        "spread"
      ]
    }
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