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  "Type": "Package",
  "Title": "Ribosome Profiling Data Analysis: from BAM to Data\nRepresentation and Interpretation",
  "Version": "1.42.0",
  "Date": "2025-07-31",
  "Author": "Alexandra Popa",
  "Maintainer": "A. Popa <alexandra.mariela.popa@gmail.com>",
  "Description": "Starting with a BAM file, this package provides the\nnecessary functions for quality assessment, read start position\nrecalibration, the counting of reads on CDS, 3'UTR, and 5'UTR,\nplotting of count data: pairs, log fold-change, codon frequency\nand coverage assessment, principal component analysis on codon\ncoverage.",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:42:04 UTC",
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    {
      "page": "aroundPromoter",
      "title": "Returns the flank size around the TSS for the x % CDSs",
      "topics": [
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      ]
    },
    {
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      "title": "Per transcript relative position of start and end codons for dataset ctrlGAlignments",
      "topics": [
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      ]
    },
    {
      "page": "codonDataCtrl",
      "title": "Codon frequency and coverage in ORFs on chromosome 1, for dataset ctrlGAlignments",
      "topics": [
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    },
    {
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      "title": "The read coverage for each codon in ORFs on chromosome 1, for dataset ctrlGAlignments",
      "topics": [
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      ]
    },
    {
      "page": "codonInfo",
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      ]
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      "topics": [
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      ]
    },
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      "title": "Apply an offset on the read start along the transcript and returns the coverage on the 5pUTR, CDS, 3pUTR, as well as a matrix of codon coverage per ORF.",
      "topics": [
        "countShiftReads"
      ]
    },
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      ]
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    },
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      "topics": [
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      ]
    },
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      ]
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      "topics": [
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      ]
    },
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      ]
    },
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      "topics": [
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      ]
    },
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      "page": "RiboProfiling",
      "title": "RiboProfiling.",
      "topics": [
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        "RiboProfiling"
      ]
    },
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      "title": "Starting from a BAM file path: quality plots, shift ribosome position, coverage on multiple transcript features and on codons.",
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