{
  "_id": "6acb680efe5cc25786e8f7a9",
  "Package": "DgeaHeatmap",
  "Title": "Implementation of Functions to Analyze Nanostring and Other Data\nfor DGE and to Generate Heatmaps",
  "Version": "0.99.3",
  "Authors@R": "c(\nperson(\"Leonie Johanna\", \"Lancelle\", role = c(\"aut\", \"cre\"),\nemail = \"leonie.lancelle@uni-bielefeld.de\",\ncomment = c(ORCID = \"0009-0004-3138-0752\"))\n)",
  "Description": "Package for data extraction from Nanostring GeoMx DSP\ndata, also works for other data. Simple functions for\nDifferential Expression Analysis. User-friendly and highly\ncustomizable functions for heatmap generation.",
  "License": "GPL-3 + file LICENSE",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "biocViews": "Clustering, DifferentialExpression, Software",
  "URL": "https://gitlab.ub.uni-bielefeld.de/spittaulab/Dgea_Heatmap_Package",
  "BugReports": "https://gitlab.ub.uni-bielefeld.de/spittaulab/Dgea_Heatmap_Package/-/issues",
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  "Repository": "https://biocstaging.r-universe.dev",
  "Date/Publication": "2026-09-11 07:57:57 UTC",
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  "Author": "Leonie Johanna Lancelle [aut, cre] (ORCID:\n<https://orcid.org/0009-0004-3138-0752>)",
  "Maintainer": "Leonie Johanna Lancelle <leonie.lancelle@uni-bielefeld.de>",
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    "build_matrix",
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    "create_contrast_matrix_edgeR",
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    "filtering_for_top_exprGenes",
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    "genRawReadCountTable",
    "get_dist",
    "get_heatmap_colors",
    "individual_matrix",
    "Kmean_generation",
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    "pairwise_contrasts",
    "performing_kMeans",
    "prepare_dge_list",
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    "row_clustering",
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    "set_annotation",
    "set_row_annotation",
    "set_sample_annotation",
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    "split_data_by_column",
    "summarise_bio_replicates",
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    {
      "page": "add_demoElem",
      "title": "Build a matrix from an input csv file, with one column as rownames",
      "topics": [
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      ]
    },
    {
      "page": "adv_Heatmap",
      "title": "Creating a color scheme based on the available color palettes of RColorBrewer for the heatmap.",
      "topics": [
        "adv_Heatmap"
      ]
    },
    {
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      "title": "Function for automatized quality control.",
      "topics": [
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      ]
    },
    {
      "page": "build_matrix",
      "title": "Builds a matrix from an input csv file, with one column as rownames",
      "topics": [
        "build_matrix"
      ]
    },
    {
      "page": "color_setting",
      "title": "Function to set color scheme for a heatmap.",
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        "color_setting"
      ]
    },
    {
      "page": "column_clustering",
      "title": "Setting the column clustering",
      "topics": [
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      ]
    },
    {
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      "title": "create_contrast_matrix_edgeR",
      "topics": [
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    },
    {
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      "title": "DGEADESeq2",
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        "DGEADESeq2"
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    {
      "page": "DGEAedgeR",
      "title": "DGEAedgeR",
      "topics": [
        "DGEAedgeR"
      ]
    },
    {
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      "title": "DGEALimma",
      "topics": [
        "DGEALimma"
      ]
    },
    {
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      "title": "Draw the advanced heatmap",
      "topics": [
        "draw_adv_heatmap"
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    },
    {
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      "title": "Function to create an elbow plot to choose k for clustering by k-Means.",
      "topics": [
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      ]
    },
    {
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      "title": "Get list of genes and their direction of regulation",
      "topics": [
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    },
    {
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      "title": "extractDEGenes",
      "topics": [
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    {
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      "title": "Function to filter a matrix to extract a chosen number of most variable rows through calculation of the variance.",
      "topics": [
        "filtering_for_top_exprGenes"
      ]
    },
    {
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      "title": "Creating a heatmap with annotation of x most variable rows(genes).",
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        "function_complexHeatmap_var"
      ]
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    {
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      "topics": [
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    {
      "page": "get_dist",
      "title": "Calculates the distance matrix",
      "topics": [
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      ]
    },
    {
      "page": "get_heatmap_colors",
      "title": "Creating a color scheme based on the available color palettes of RColorBrewer for the heatmap.",
      "topics": [
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    },
    {
      "page": "individual_matrix",
      "title": "Creates a matrix only containing chosen columns of an original matrix with more data.",
      "topics": [
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      ]
    },
    {
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      "title": "Generates K-means for the columns and rows of a matrix.",
      "topics": [
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      ]
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      "topics": [
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      "title": "Create pairwise contrasts",
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