Package: tadar
Title: Transcriptome Analysis of Differential Allelic Representation
Version: 1.9.0
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, Seqinfo, Gviz, IRanges, lifecycle,
        MatrixGenerics, methods, rlang, Rsamtools, S4Vectors, stats,
        VariantAnnotation
Suggests: BiocStyle, covr, knitr, limma, rmarkdown, testthat (>=
        3.0.0), tidyverse
Config/pak/sysreqs: make libbz2-dev libicu-dev libjpeg-dev liblzma-dev
        libpng-dev libxml2-dev libssl-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:25:24 UTC
RemoteUrl: https://github.com/bioc/tadar
RemoteRef: HEAD
RemoteSha: 7b054488528c6d728a365c648b1baf29427a7a81
NeedsCompilation: no
Packaged: 2025-11-13 07:25:00 UTC; root
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 4.6.0; ; 2025-11-13 07:28:47 UTC; windows
