{
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  "Title": "HiPathia: High-throughput Pathway Analysis",
  "Version": "3.13.0",
  "Authors@R": "c(person(\"Marta R.\", \"Hidalgo\", email = \"marta.hidalgo@outlook.es\", role = c(\"aut\", \"cre\")),\nperson(\"José\", \"Carbonell-Caballero\", role = c(\"ctb\")),\nperson(\"Francisco\", \"Salavert\", role = c(\"ctb\")),\nperson(\"Alicia\", \"Amadoz\", role = c(\"ctb\")),\nperson(\"Çankut\", \"Cubuk\", role = c(\"ctb\")),\nperson(\"Joaquin\", \"Dopazo\", role = c(\"ctb\")))",
  "Description": "Hipathia is a method for the computation of signal\ntransduction along signaling pathways from transcriptomic data.\nThe method is based on an iterative algorithm which is able to\ncompute the signal intensity passing through the nodes of a\nnetwork by taking into account the level of expression of each\ngene and the intensity of the signal arriving to it. It also\nprovides a new approach to functional analysis allowing to\ncompute the signal arriving to the functions annotated to each\npathway.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:47:49 UTC",
  "RemoteUrl": "https://github.com/bioc/hipathia",
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  "Author": "Marta R. Hidalgo [aut, cre],\nJosé Carbonell-Caballero [ctb],\nFrancisco Salavert [ctb],\nAlicia Amadoz [ctb],\nÇankut Cubuk [ctb],\nJoaquin Dopazo [ctb]",
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      "title": "Create visualization HTML",
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      "title": "Compares the gene expression, pathway activation level and the function activation level of the",
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    },
    {
      "page": "DAdata",
      "title": "Wilcoxon and limma comparison object for nodes, pathways and functional annotations",
      "topics": [
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      "title": "Table and plot of total number of altered and not altered nodes, paths and functions (Uniprot keywords and/or GO terms, if present).",
      "topics": [
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      "page": "DAreport",
      "title": "Create visualization HTML",
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      "title": "Lists and plots the top 'n' altered pathways, taking into account the number of altered .",
      "topics": [
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    {
      "page": "DAtop",
      "title": "Lists and plots the top 'n' altered nodes, paths and functions (Uniprot keywords and/or GO terms, if present).",
      "topics": [
        "DAtop"
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    },
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      "page": "define_colors",
      "title": "Color palettes to be used in plots.",
      "topics": [
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      "title": "Performs a Principal Components Analysis",
      "topics": [
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    },
    {
      "page": "do_wilcoxon",
      "title": "Apply Wilcoxon test",
      "topics": [
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      "page": "exp_data",
      "title": "Normalized BRCA gene expression dataset",
      "topics": [
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      "page": "get_file",
      "title": "Loads a RData object and downloads it from Zenodo if necessary",
      "topics": [
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    {
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      "topics": [
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    },
    {
      "page": "get_highest_sig_ancestor",
      "title": "Get highest common GO ancestor of GO annotations",
      "topics": [
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    {
      "page": "get_node_names",
      "title": "Tranlates node IDs to node names",
      "topics": [
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    {
      "page": "get_nodes_data",
      "title": "Gets the object of node activation values",
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    },
    {
      "page": "get_path_names",
      "title": "Tranlates path IDs to path names",
      "topics": [
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    {
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      "title": "Gets the object of subpathway activation values",
      "topics": [
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    },
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      "topics": [
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    },
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      "page": "get_pathways_annotations",
      "title": "Get Pathways functional annotations",
      "topics": [
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      "title": "Compute pathway summary",
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      "title": "Gene Ontology matrix of the BRCA gene expression dataset",
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      "title": "Plots subpathways heatmap",
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      "title": "Head function for SummarizedExperiment, data.frames and matrix objects",
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      "page": "hidata",
      "title": "Results object",
      "topics": [
        "hidata"
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    },
    {
      "page": "hipathia",
      "title": "Computes the level of activation of the subpathways for each of the samples",
      "topics": [
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    },
    {
      "page": "igraphs_upgrade",
      "title": "Upgrade igraphs to current version",
      "topics": [
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      "page": "is_accepted_species",
      "title": "Checks whether a species is accepted",
      "topics": [
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    {
      "page": "load_annofuns",
      "title": "Loads annotations object",
      "topics": [
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      "page": "load_annots",
      "title": "Loads functional annotations to genes",
      "topics": [
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      "page": "load_entrez_hgnc",
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      "topics": [
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      "page": "load_gobp_net",
      "title": "Loads GO graph",
      "topics": [
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      "page": "load_mgi",
      "title": "Loads object with graph information",
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      "page": "load_pathways",
      "title": "Loads the pathways object.",
      "topics": [
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    },
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      "topics": [
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    {
      "page": "load_xref",
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      "topics": [
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    },
    {
      "page": "mgi_from_sif",
      "title": "Create a Pathways object from SIF files",
      "topics": [
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    {
      "page": "multiple_pca_plot",
      "title": "Plots multiple components of a PCA",
      "topics": [
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    },
    {
      "page": "node_color",
      "title": "Get colors of the nodes from a comparison file",
      "topics": [
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    },
    {
      "page": "node_color_per_de",
      "title": "Colors of the nodes by its differential expression",
      "topics": [
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    },
    {
      "page": "normalize_data",
      "title": "Normalize expression data from a SummarizedExperiment or matrix to be used in 'hipathia'",
      "topics": [
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    },
    {
      "page": "normalize_paths",
      "title": "Normalize the pathway matrix by rows",
      "topics": [
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    },
    {
      "page": "path_vals",
      "title": "Pathways matrix of the BRCA gene expression dataset",
      "topics": [
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    },
    {
      "page": "paths_to_go_ancestor",
      "title": "Create path results table with highest significant GO ancestors",
      "topics": [
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    },
    {
      "page": "pathway_comparison_plot",
      "title": "Plots pathway with colored significant paths",
      "topics": [
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    },
    {
      "page": "pathways",
      "title": "Pathways object including pathways has03320 and hsa04012.",
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    {
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      "title": "Plots two components of a PCA",
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    {
      "page": "plotVG",
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      "topics": [
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    },
    {
      "page": "quantify_terms",
      "title": "Computes the level of activation of the functions related to the previously computed subpathways",
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    {
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    },
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    {
      "page": "visualize_report",
      "title": "Visualize a HiPathia report",
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      "source": "hipathia-vignette.Rmd",
      "filename": "hipathia-vignette.html",
      "title": "Hipathia Package",
      "author": "Marta R. Hidalgo, Francisco Salavert, Alicia Amadoz, Çankut Cubuk, José Carbonell-Caballero, Joaquín Dopazo",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2017-11-27 15:37:48",
      "modified": "2026-03-20 14:01:28",
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