{
  "_id": "6a168ef7acfb0bcc41d77ec6",
  "Package": "broadSeq",
  "Title": "broadSeq : for streamlined exploration of RNA-seq data",
  "Version": "1.7.0",
  "Authors@R": "person(\"Rishi\", \"Das Roy\", , \"rishi.dasroy@gmail.com\", role = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-3276-7279\"))",
  "Description": "This package helps user to do easily RNA-seq data analysis\nwith multiple methods (usually which needs many different input\nformats). Here the user will provid the expression data as a\nSummarizedExperiment object and will get results from different\nmethods. It will help user to quickly evaluate different\nmethods.",
  "License": "MIT + file LICENSE",
  "URL": "https://github.com/dasroy/broadSeq",
  "BugReports": "https://github.com/dasroy/broadSeq/issues",
  "Encoding": "UTF-8",
  "Roxygen": "list(markdown = TRUE)",
  "RoxygenNote": "7.2.3",
  "biocViews": "GeneExpression, DifferentialExpression, RNASeq,\nTranscriptomics, Sequencing, Coverage, GeneSetEnrichment, GO",
  "VignetteBuilder": "knitr",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev libglpk-dev make libicu-dev libpng-dev\nlibuv1-dev libxml2-dev libssl-dev perl libnode-dev zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:03:13 UTC",
  "RemoteUrl": "https://github.com/bioc/broadSeq",
  "RemoteRef": "HEAD",
  "RemoteSha": "4cc0a2176662e55b5fd52028e426b07f3df3847a",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-27 06:18:51 UTC",
    "User": "root"
  },
  "Author": "Rishi Das Roy [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-3276-7279>)",
  "Maintainer": "Rishi Das Roy <rishi.dasroy@gmail.com>",
  "MD5sum": "bb71f5eaa255017ce7b3602435dc5e99",
  "_user": "bioc",
  "_type": "src",
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  "_published": "2026-05-27T06:28:07.613Z",
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    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
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    "email": "rishi.dasroy@gmail.com",
    "login": "vondorishi",
    "description": "",
    "uuid": 6110508,
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  "_registered": true,
  "_dependencies": [
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  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
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  "_tags": [],
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    "differentialexpression",
    "rnaseq",
    "transcriptomics",
    "sequencing",
    "coverage",
    "genesetenrichment",
    "go"
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  "_stars": 9,
  "_contributors": [
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  "_userbio": {
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    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
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    "source": "https://www.bioconductor.org/packages/stats/bioc/broadSeq"
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  "_devurl": "https://github.com/dasroy/broadseq",
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  "_rbuild": "4.6.0",
  "_assets": [
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    "extra/citation.cff",
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    "extra/contents.json",
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  "_homeurl": "https://github.com/dasroy/broadseq",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "assay_plot",
    "biplotAnyPC",
    "combinedEnrichment",
    "genes_plot",
    "getFeatureLoadRanking",
    "normalizeEdgerCPM",
    "plot_MDS",
    "plotAnyPC",
    "plotHeatmapCluster",
    "prcompTidy",
    "round_df",
    "sampleAssay_plot",
    "transformDESeq2",
    "use_DELocal",
    "use_deseq2",
    "use_EBSeq",
    "use_edgeR",
    "use_edgeR_exact",
    "use_edgeR_GLM",
    "use_limma",
    "use_limma_trend",
    "use_limma_voom",
    "use_multDE",
    "use_NOIseq",
    "volcanoPlot"
  ],
  "_help": [
    {
      "page": "broadSeq-package",
      "title": "broadSeq : for streamlined exploration of RNA-seq data",
      "topics": [
        "broadSeq-package",
        "broadSeq"
      ]
    },
    {
      "page": "combinedEnrichment",
      "title": "Provides GO gene set enrichment and over-representation analysis",
      "topics": [
        "combinedEnrichment"
      ]
    },
    {
      "page": "genes_plot",
      "title": "Expression of multiple genes/features from a single assay as boxplot (or added dotplot)",
      "topics": [
        "assay_plot",
        "genes_plot"
      ]
    },
    {
      "page": "normalizeEdgerCPM",
      "title": "Use of edgeR package to normalize count data",
      "topics": [
        "normalizeEdgerCPM"
      ]
    },
    {
      "page": "plot_MDS",
      "title": "Classical multidimensional scaling",
      "topics": [
        "plot_MDS"
      ]
    },
    {
      "page": "plotHeatmapCluster",
      "title": "Plot clustered heatmaps",
      "topics": [
        "plotHeatmapCluster"
      ]
    },
    {
      "page": "prcompTidy",
      "title": "Perform Principal Components Analysis",
      "topics": [
        "biplotAnyPC",
        "getFeatureLoadRanking",
        "plotAnyPC",
        "prcompTidy"
      ]
    },
    {
      "page": "round_df",
      "title": "Applies round function only on numeric columns of a data.frame.",
      "topics": [
        "round_df"
      ]
    },
    {
      "page": "sampleAssay_plot",
      "title": "Useful to visualize distribution of assay values for each sample. Plots 'boxplot' of any assay for each sample. Aesthetic can be added from colData.",
      "topics": [
        "sampleAssay_plot"
      ]
    },
    {
      "page": "transformDESeq2",
      "title": "Transform SummarizedExperiment with DESeq2 package",
      "topics": [
        "transformDESeq2"
      ]
    },
    {
      "page": "use_DELocal",
      "title": "To use SummarizedExperiment with package DELocal",
      "topics": [
        "use_DELocal"
      ]
    },
    {
      "page": "use_deseq2",
      "title": "To use SummarizedExperiment with package DESeq2",
      "topics": [
        "use_deseq2"
      ]
    },
    {
      "page": "use_EBSeq",
      "title": "To use SummarizedExperiment with package EBSeq",
      "topics": [
        "use_EBSeq"
      ]
    },
    {
      "page": "use_edgeR",
      "title": "To use SummarizedExperiment with package edgeR",
      "topics": [
        "use_edgeR",
        "use_edgeR_exact",
        "use_edgeR_GLM"
      ]
    },
    {
      "page": "use_limma",
      "title": "To use SummarizedExperiment with package limma",
      "topics": [
        "use_limma",
        "use_limma_trend",
        "use_limma_voom"
      ]
    },
    {
      "page": "use_multDE",
      "title": "To identify differentially expressed genes by multiple methods",
      "topics": [
        "use_multDE"
      ]
    },
    {
      "page": "use_NOIseq",
      "title": "Differential expression method for NOISeq",
      "topics": [
        "use_NOIseq"
      ]
    },
    {
      "page": "use_SAMseq",
      "title": "To use SummarizedExperiment with package samr",
      "topics": [
        "use_SAMseq"
      ]
    },
    {
      "page": "volcanoPlot",
      "title": "Volcano plot with formatted x and y axis label.",
      "topics": [
        "volcanoPlot"
      ]
    }
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      "filename": "broadSeq.html",
      "title": "Using broadSeq to analyze RNA-seq data",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Reading the data",
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        "access",
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      "created": "2024-03-08 12:41:55",
      "modified": "2025-06-25 14:34:18",
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