Package: tadar
Title: Transcriptome Analysis of Differential Allelic Representation
Version: 1.6.0
Description: This package provides functions to standardise the analysis of
    Differential Allelic Representation (DAR). DAR compromises the integrity of
    Differential Expression analysis results as it can bias expression,
    influencing the classification of genes (or transcripts) as being
    differentially expressed. DAR analysis results in an easy-to-interpret
    value between 0 and 1 for each genetic feature of interest, where 0
    represents identical allelic representation and 1 represents complete
    diversity. This metric can be used to identify features prone to
    false-positive calls in Differential Expression analysis, and can be
    leveraged with statistical methods to alleviate the impact of such
    artefacts on RNA-seq data.
Authors@R: 
    c(person("Lachlan", "Baer",
        email = "baerlachlan@gmail.com",
        role = c("aut", "cre"),
        comment = c(ORCID = "0000-0001-5213-3401")),
    person("Stevie", "Pederson",
        email = "stephen.pederson.au@gmail.com",
        role = "aut",
        comment = c(ORCID = "0000-0001-8197-3303")))
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
Config/testthat/edition: 3
BugReports: https://github.com/baerlachlan/tadar/issues
URL: https://github.com/baerlachlan/tadar
BiocType: Software
biocViews: Sequencing, RNASeq, SNP, GenomicVariation,
        VariantAnnotation, DifferentialExpression
VignetteBuilder: knitr
Depends: GenomicRanges, ggplot2, R (>= 4.4.0)
Imports: BiocGenerics, GenomeInfoDb, Gviz, IRanges, lifecycle,
        MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats,
        VariantAnnotation
Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>=
        3.0.0), tidyverse
git_url: https://git.bioconductor.org/packages/tadar
git_branch: RELEASE_3_21
git_last_commit: fa8aa7e
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: no
Packaged: 2025-04-16 04:08:13 UTC; biocbuild
Author: Lachlan Baer [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-5213-3401>),
  Stevie Pederson [aut] (ORCID: <https://orcid.org/0000-0001-8197-3303>)
Maintainer: Lachlan Baer <baerlachlan@gmail.com>
Built: R 4.5.0; ; 2025-04-16 15:41:11 UTC; windows
