{
  "_id": "6a1aae441d7bb097a09d4e6d",
  "Package": "ribosomeProfilingQC",
  "Type": "Package",
  "Title": "Ribosome Profiling Quality Control",
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  "Authors@R": "c(person(given=\"Jianhong\", family=\"Ou\", email=\"jou@morgridge.org\", \nrole=c(\"aut\", \"cre\"), comment=c(ORCID=\"0000-0002-8652-2488\")),\nperson(given=\"Mariah\", family=\"Hoye\", email=\"mariah.hoye@duke.edu\",\nrole=c(\"aut\")))",
  "Description": "Ribo-Seq (also named ribosome profiling or footprinting)\nmeasures translatome (unlike RNA-Seq, which sequences the\ntranscriptome) by direct quantification of the\nribosome-protected fragments (RPFs). This package provides the\ntools for quality assessment of ribosome profiling. In\naddition, it can preprocess Ribo-Seq data for subsequent\ndifferential analysis.",
  "License": "GPL (>=3) + file LICENSE",
  "Encoding": "UTF-8",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:51:55 UTC",
  "RemoteUrl": "https://github.com/bioc/ribosomeProfilingQC",
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  "Author": "Jianhong Ou [aut, cre] (ORCID: <https://orcid.org/0000-0002-8652-2488>),\nMariah Hoye [aut]",
  "Maintainer": "Jianhong Ou <jou@morgridge.org>",
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    "codonBias",
    "codonUsage",
    "countReads",
    "coverageDepth",
    "coverageRates",
    "cvgd",
    "estimatePsite",
    "filterCDS",
    "FLOSS",
    "frameCounts",
    "getFPKM",
    "getORFscore",
    "getPsiteCoordinates",
    "metaPlot",
    "normalizeTEbyLoess",
    "normBy",
    "normByRUVs",
    "PAmotif",
    "plotDistance2Codon",
    "plotFrameDensity",
    "plotSpliceEvent",
    "plotTE",
    "plotTranscript",
    "prepareCDS",
    "readsDistribution",
    "readsEndPlot",
    "readsLenToKeep",
    "ribosomeReleaseScore",
    "shiftReadsByFrame",
    "show",
    "simulateRPF",
    "spliceEvent",
    "strandPlot",
    "summaryReadsLength",
    "translationalEfficiency"
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  "_help": [
    {
      "page": "assignReadingFrame",
      "title": "Assign reading frame",
      "topics": [
        "assignReadingFrame"
      ]
    },
    {
      "page": "codonBias",
      "title": "Codon usage bias",
      "topics": [
        "codonBias"
      ]
    },
    {
      "page": "codonUsage",
      "title": "Start or Stop codon usage",
      "topics": [
        "codonUsage"
      ]
    },
    {
      "page": "countReads",
      "title": "Extract counts for RPFs and RNAs",
      "topics": [
        "countReads"
      ]
    },
    {
      "page": "coverageDepth",
      "title": "Extract coverage depth for gene level or transcript level",
      "topics": [
        "coverageDepth"
      ]
    },
    {
      "page": "coverageRates",
      "title": "Calculate coverage rate",
      "topics": [
        "coverageRates"
      ]
    },
    {
      "page": "cvgd-class",
      "title": "Class '\"cvgd\"'",
      "topics": [
        "$,cvgd-method",
        "$<-,cvgd-method",
        "cvgd",
        "cvgd-class",
        "show,cvgd-method",
        "[[,cvgd,ANY,ANY-method",
        "[[<-,cvgd,ANY,ANY,ANY-method"
      ]
    },
    {
      "page": "estimatePsite",
      "title": "Estimate P site position",
      "topics": [
        "estimatePsite"
      ]
    },
    {
      "page": "filterCDS",
      "title": "Filter CDS by size",
      "topics": [
        "filterCDS"
      ]
    },
    {
      "page": "FLOSS",
      "title": "Fragment Length Organization Similarity Score (FLOSS)",
      "topics": [
        "FLOSS"
      ]
    },
    {
      "page": "frameCounts",
      "title": "Extract counts for gene level or transcript level",
      "topics": [
        "frameCounts"
      ]
    },
    {
      "page": "getFPKM",
      "title": "Get FPKM values for counts",
      "topics": [
        "getFPKM"
      ]
    },
    {
      "page": "getORFscore",
      "title": "Calculate ORFscore",
      "topics": [
        "getORFscore"
      ]
    },
    {
      "page": "getPsiteCoordinates",
      "title": "Get P site coordinates",
      "topics": [
        "getPsiteCoordinates"
      ]
    },
    {
      "page": "ggBar",
      "title": "barplot by ggplot2",
      "topics": [
        "ggBar"
      ]
    },
    {
      "page": "metaPlot",
      "title": "Metagene analysis plot",
      "topics": [
        "metaPlot"
      ]
    },
    {
      "page": "normalizeTEbyLoess",
      "title": "Normalize the TE by Loess",
      "topics": [
        "normalizeTEbyLoess"
      ]
    },
    {
      "page": "normBy",
      "title": "Normalization by edgeR, DESeq2 or RUVSeq",
      "topics": [
        "normBy"
      ]
    },
    {
      "page": "normByRUVs",
      "title": "Normalization by RUVSeq",
      "topics": [
        "normByRUVs"
      ]
    },
    {
      "page": "PAmotif",
      "title": "Metaplot of P site distribution",
      "topics": [
        "PAmotif"
      ]
    },
    {
      "page": "plotDistance2Codon",
      "title": "Metaplot of P site distribution",
      "topics": [
        "plotDistance2Codon"
      ]
    },
    {
      "page": "plotFrameDensity",
      "title": "Plot density for each reading frame",
      "topics": [
        "plotFrameDensity"
      ]
    },
    {
      "page": "plotSpliceEvent",
      "title": "Plot splice event",
      "topics": [
        "plotSpliceEvent"
      ]
    },
    {
      "page": "plotTE",
      "title": "Plot translational efficiency",
      "topics": [
        "plotTE"
      ]
    },
    {
      "page": "plotTranscript",
      "title": "Plot reads P site abundance for a specific transcript",
      "topics": [
        "plotTranscript"
      ]
    },
    {
      "page": "prepareCDS",
      "title": "Prepare CDS",
      "topics": [
        "prepareCDS"
      ]
    },
    {
      "page": "readsDistribution",
      "title": "Plot reads distribution in genomic elements",
      "topics": [
        "readsDistribution"
      ]
    },
    {
      "page": "readsEndPlot",
      "title": "Plot start/stop windows",
      "topics": [
        "readsEndPlot"
      ]
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      "page": "readsLenToKeep",
      "title": "Get reads length to keep by cutoff percentage",
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      "title": "Ribosome Release Score (RRS)",
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      "title": "Shift reads by reading frame",
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      "title": "Get splicing events",
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      "page": "strandPlot",
      "title": "Plot the distribution of reads in sense and antisense strand",
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      "page": "summaryReadsLength",
      "title": "Summary the reads lengths",
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    },
    {
      "page": "translationalEfficiency",
      "title": "Translational Efficiency",
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    }
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  "_vignettes": [
    {
      "source": "ribosomeProfilingQC.Rmd",
      "filename": "ribosomeProfilingQC.html",
      "title": "ribosomeProfilingQC Guide",
      "author": "Jianhong Ou, Mariah Hoye",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Quick start",
        "Load genome",
        "Prepare annotaiton CDS",
        "Inputs",
        "Estimate P site",
        "Plot start/stop windows",
        "Read all P site coordinates",
        "Fragment size distribution",
        "Filter the reads by fragment size",
        "Sense/antisense strand plot",
        "Genomic element distribution",
        "Metagene analysis plot for 5'UTR/CDS/3'UTR",
        "Reading frame",
        "ORFscore vs coverageRate",
        "Bad case",
        "Prepare for downstream analysis",
        "RPFs only",
        "Count for RPFs",
        "Differential analysis only for RPFs",
        "Alternative splicing, translation initiation and polyadenylation",
        "RPFs and RNA-seq",
        "By counts",
        "Count for RPFs and RNA-seq",
        "Translational Efficiency (TE)",
        "Differential analysis for TE",
        "By coverage",
        "Maximum N-mer translational efficiency",
        "Ribosome Release Score (RRS)",
        "Metagene analysis plot",
        "Fragment Length Organization Similarity Score (FLOSS) [@ingolia2014ribosome]",
        "References"
      ],
      "created": "2019-10-29 13:33:37",
      "modified": "2025-05-02 14:13:01",
      "commits": 21
    }
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