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  "Title": "Pathway Enrichment Analysis Based on Bayesian Network",
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  "Authors@R": "c(person(\"Samaneh\",\"Maleknia\",role = c(\"aut\",\"cre\"),email = \"maleknias@gmail.com\"),person(\"Mohsen\",\"Namazi\",role = \"aut\"),person(\"Kaveh\",\"Kavousi\",role = c(\"ctb\")),person(\"Ali\",\"Sharifi-Zarchi\",role = c(\"ctb\")),person(\"Vahid\",\"Rezaei-Tabar\",role = c(\"ctb\")))",
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  "Description": "Maleknia et al. (2020) <doi:10.1101/2020.01.13.905448>. A\nnovel pathway enrichment analysis package based on Bayesian\nnetwork to investigate the topology features of the pathways.\nfirstly, 187 kyoto encyclopedia of genes and genomes (KEGG)\nhuman non-metabolic pathways which their cycles were eliminated\nby biological approach, enter in analysis as Bayesian network\nstructures. The constructed Bayesian network were optimized by\nthe Least Absolute Shrinkage Selector Operator (lasso) and the\nparameters were learned based on gene expression data. Finally,\nthe impacted pathways were enriched by Fisher’s Exact Test on\nsignificant parameters.",
  "biocViews": "NetworkEnrichment, GeneExpression, Pathways, Bayesian, KEGG",
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  "Repository": "https://samaneh-bioinformatics.r-universe.dev",
  "Date/Publication": "2020-04-04 07:37:58 UTC",
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      "page": "BN_struct",
      "title": "Construct Bayesian networks structures",
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      "page": "BNrich",
      "title": "Analysis of significant final BNs",
      "topics": [
        "BNrich"
      ]
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      "page": "esti_par",
      "title": "Estimate parameters of BNs in control and disease states",
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        "esti_par"
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    },
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      "title": "Download data file",
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    {
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    {
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      "title": "Testing the equality regression coefficients",
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      "title": "Simplification networks - applied to unifying nodes",
      "topics": [
        "unify_path"
      ]
    },
    {
      "page": "var_mat",
      "title": "Estimate variance-covariance matrixes for any parameters of BNs",
      "topics": [
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    }
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      "title": "BNrich: A Novel Pathway Enrichment Analysis Based on Bayesian Network",
      "author": "Samaneh Maleknia*(1),Mohsen Namazi(1),Kaveh Kavousi(1),Ali Sharifi-Zarchi(2),Vahid Rezaei Tabar(3)",
      "engine": "knitr::knitr",
      "headings": [
        "Abstract:",
        "Introduction",
        "Quick Start",
        "Install BNrich",
        "prepare essential data",
        "Unify data, the first step of simplification",
        "BN: construct structures and estimate parameters",
        "construct BN structures",
        "The LASSO regression, the second step of simplification",
        "Estimate the BN parameters",
        "Testing the equality BNs parameters",
        "Variance of BNs parameters",
        "Identification of enriched pathways",
        "Session Info",
        "References:"
      ],
      "created": "2019-08-31 15:18:13",
      "modified": "2020-03-24 08:20:24",
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