{
  "_id": "6a21f43dcd65a98ecbd42a47",
  "Package": "profileplyr",
  "Type": "Package",
  "Title": "Visualization and annotation of read signal over genomic ranges\nwith profileplyr",
  "Version": "1.29.3",
  "Date": "2025-07-22",
  "Authors@R": "c(\nperson(\"Doug\", \"Barrows\", email = \"doug.barrows@gmail.com\", role = c(\"aut\", \"cre\")),\nperson(\"Tom\", \"Carroll\", email = \"tc.infomatics@gmail.com\", role = \"aut\"))",
  "Description": "Quick and straightforward visualization of read signal\nover genomic intervals is key for generating hypotheses from\nsequencing data sets (e.g. ChIP-seq, ATAC-seq,\nbisulfite/methyl-seq). Many tools both inside and outside of R\nand Bioconductor are available to explore these types of data,\nand they typically start with a bigWig or BAM file and end with\nsome representation of the signal (e.g. heatmap). profileplyr\nleverages many Bioconductor tools to allow for both flexibility\nand additional functionality in workflows that end with\nvisualization of the read signal.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-06-04 17:48:57 UTC",
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    "Date": "2026-06-04 21:41:18 UTC",
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  "Author": "Doug Barrows [aut, cre],\nTom Carroll [aut]",
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      "page": "annotateRanges",
      "title": "Annotate profileplyr ranges to genes using ChIPseeker",
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        "convertToEnrichedHeatmapMat,profileplyr-method"
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    "xtable",
    "XVector",
    "yaml",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "profileplyr.Rmd",
      "filename": "profileplyr.html",
      "title": "Visualization and annotation of read signal over genomic ranges with profileplyr",
      "author": "Doug Barrows and Tom Carroll",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Import signal quantification from deepTools or soGGi",
        "Starting with output from deepTools 'computeMatrix'",
        "Starting with output from soGGi",
        "The profileplyr object",
        "Key components of the object",
        "Subsetting the profileplyr object",
        "Changing sample names",
        "Connecting profileplyr functions using the pipe (%>%) operator",
        "Export/Conversion of profileplyr object for heatmap visualization of ranges",
        "Export to a deepTools matrix",
        "Directly generate a customized EnrichedHeatmap with annotated ranges",
        "Convert to an EnrichedHeatmap matrix",
        "Summarize signal for ggplot or heatmap visualization",
        "Matrix output for heatmaps",
        "Long output for ggplot",
        "profileplyr object output with summarized matrix",
        "Annotating of genomic ranges with clusters, genomic regions, and genes",
        "K-means and hierarchical clustering of the genomic ranges",
        "Output matrix with cluster information to deepTools",
        "Generate group-annotated heatmap in R directly with generateEnrichedHeatmap()",
        "Visualize mean range signal for each cluster with ggplot",
        "Gene annotation of ranges",
        "Annotation of ranges with genes and genomic regions using ChIPseeker",
        "Adding metadata information beyond the grouping column to the EnrichedHeatmap",
        "Annotation of ranges with genes using GREAT",
        "Grouping ranges by range metadata, gene list, or additional GRanges",
        "Switch output grouping columns within existing range metadata",
        "Group by user-supplied GRanges",
        "Group by user-supplied gene list",
        "Gene set list contains a character data",
        "Gene set list with data frames for heatmap annotation (using pipe - %>%)",
        "Combining multiple profileplyr functions for heatmap annotation",
        "Acknowledgements",
        "Session info"
      ],
      "created": "2019-04-10 05:02:34",
      "modified": "2022-10-10 19:35:00",
      "commits": 15
    }
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  "_nocasepkg": "profileplyr",
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