{
  "_id": "6a1b04ce1d7bb097a0a02afa",
  "Package": "segmenter",
  "Type": "Package",
  "Title": "Perform Chromatin Segmentation Analysis in R by Calling ChromHMM",
  "Version": "1.18.0",
  "Description": "Chromatin segmentation analysis transforms ChIP-seq data\ninto signals over the genome. The latter represents the\nobserved states in a multivariate Markov model to predict the\nchromatin's underlying states. ChromHMM, written in Java,\nintegrates histone modification datasets to learn the chromatin\nstates de-novo. The goal of this package is to call chromHMM\nfrom within R, capture the output files in an S4 object and\ninterface to other relevant Bioconductor analysis tools. In\naddition, segmenter provides functions to test, select and\nvisualize the output of the segmentation.",
  "Authors@R": "person(\"Mahmoud\", \"Ahmed\",\nemail = \"mahmoud.s.fahmy@students.kasralainy.edu.eg\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0002-4377-6541\"))",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:56:25 UTC",
  "RemoteUrl": "https://github.com/bioc/segmenter",
  "RemoteRef": "RELEASE_3_23",
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  "Packaged": {
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    "User": "root"
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  "Author": "Mahmoud Ahmed [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-4377-6541>)",
  "Maintainer": "Mahmoud Ahmed <mahmoud.s.fahmy@students.kasralainy.edu.eg>",
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      "title": "A segmentation object generated from the test data",
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      "table": false,
      "tojson": false
    },
    {
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      "object": "test_objs",
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      "title": "Call Java 'BinarizeBed'",
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      ]
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    {
      "page": "dot-LearnModel",
      "title": "Call Java 'LearnModel'",
      "topics": [
        ".LearnModel"
      ]
    },
    {
      "page": "accessors",
      "title": "Accessors for the 'segmentation' objects",
      "topics": [
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        "bins",
        "bins,segmentation-method",
        "cells",
        "cells,segmentation-method",
        "counts",
        "counts,segmentation-method",
        "emission",
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        "likelihood",
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        "transition",
        "transition,segmentation-method",
        "TSS",
        "TSS,segmentation-method"
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    {
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      "topics": [
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    },
    {
      "page": "binarize_bam",
      "title": "Binarize the bam files",
      "topics": [
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    },
    {
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      "title": "Binarize the bed files",
      "topics": [
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    },
    {
      "page": "compare_models",
      "title": "Compare two or more models",
      "topics": [
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    },
    {
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      "title": "Count reads in 'GRanges' objects from bam files",
      "topics": [
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    },
    {
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      "title": "Make emissions file name",
      "topics": [
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      ]
    },
    {
      "page": "enrichment_files",
      "title": "Make enrichment file names",
      "topics": [
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    },
    {
      "page": "get_frequency",
      "title": "Get the frequency of the segments in each cell type",
      "topics": [
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    },
    {
      "page": "get_width",
      "title": "Get the width of the segments in each cell type",
      "topics": [
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    },
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      "topics": [
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    },
    {
      "page": "merge_segments_bins",
      "title": "Merge segments and bins objects",
      "topics": [
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    },
    {
      "page": "methods",
      "title": "Methods to interact with 'segmentation' objects",
      "topics": [
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        "show,segmentation-method"
      ]
    },
    {
      "page": "model_file",
      "title": "Make model file name",
      "topics": [
        "model_file"
      ]
    },
    {
      "page": "overlap_files",
      "title": "Make overlap file names",
      "topics": [
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    {
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      "title": "Format the loaded binarized data",
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      "headings": [
        "Overview",
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        "Inputs",
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