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  "Package": "tadar",
  "Title": "Transcriptome Analysis of Differential Allelic Representation",
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  "Description": "This package provides functions to standardise the\nanalysis of Differential Allelic Representation (DAR). DAR\ncompromises the integrity of Differential Expression analysis\nresults as it can bias expression, influencing the\nclassification of genes (or transcripts) as being\ndifferentially expressed. DAR analysis results in an\neasy-to-interpret value between 0 and 1 for each genetic\nfeature of interest, where 0 represents identical allelic\nrepresentation and 1 represents complete diversity. This metric\ncan be used to identify features prone to false-positive calls\nin Differential Expression analysis, and can be leveraged with\nstatistical methods to alleviate the impact of such artefacts\non RNA-seq data.",
  "Authors@R": "c(person(\"Lachlan\", \"Baer\",\nemail = \"baerlachlan@gmail.com\",\nrole = c(\"aut\", \"cre\"),\ncomment = c(ORCID = \"0000-0001-5213-3401\")),\nperson(\"Stevie\", \"Pederson\",\nemail = \"stephen.pederson.au@gmail.com\",\nrole = \"aut\",\ncomment = c(ORCID = \"0000-0001-8197-3303\")))",
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  "URL": "https://github.com/baerlachlan/tadar",
  "BiocType": "Software",
  "biocViews": "Sequencing, RNASeq, SNP, GenomicVariation,\nVariantAnnotation, DifferentialExpression",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 13:01:33 UTC",
  "RemoteUrl": "https://github.com/bioc/tadar",
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  "Author": "Lachlan Baer [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-5213-3401>),\nStevie Pederson [aut] (ORCID: <https://orcid.org/0000-0001-8197-3303>)",
  "Maintainer": "Lachlan Baer <baerlachlan@gmail.com>",
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    "flipRanges",
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      "title": "Genomic feature example data",
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      "file": "chr1_genes.rda",
      "class": [
        "GRanges"
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      "title": "Assign DAR values to genomic features",
      "topics": [
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        "assignFeatureDar,GRangesList,GRanges-method"
      ]
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      "title": "Genomic feature example data",
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      "title": "Differential expression example data",
      "topics": [
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      ]
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      "title": "Count alleles within each experimental group",
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        "countAlleles,GRanges,list-method"
      ]
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    {
      "page": "countsToProps-methods",
      "title": "Convert allele counts to proportions",
      "topics": [
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        "countsToProps,GRangesList-method"
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      "page": "dar-methods",
      "title": "Calculate Differential Allelic Representation (DAR)",
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        "dar,GRangesList,matrix-method"
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        "filterLoci,GRangesList-method"
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    },
    {
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      "title": "Convert DAR origin ranges to DAR region ranges, or vice versa",
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        "flipRanges,GRangesList-method"
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    },
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      "title": "DAR-moderated _p_-values",
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        "modP,numeric,numeric-method"
      ]
    },
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      "title": "Plot DAR across a chromosome",
      "topics": [
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        "plotChrDar,GRanges-method"
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    },
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      "title": "Plot the Empirical Cumulative Distribution Function of DAR",
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        "plotDarECDF,GRanges-method"
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      "title": "Differential Allelic Representation (DAR) analysis",
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