darr

[baerlachlan]

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• Repository: https://github.com/baerlachlan/darr

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[bioc-issue-bot]

Hi @baerlachlan

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: darr
Title: Differential Allelic Representation
Version: 0.99.0
Description: This package provides functions to standardise the analysis of
    Differential Allelic Representation (DAR). DAR analysis is intended to
    be performed on genotype calls from variant discovery software, resulting
    in a metric that represents the allelic diversity between groups of samples
    at each SNP locus. The DAR metric provides a good estimate for the
    possibility of expression quantitative trait loci differences between
    sample groups, which may contribute to unexpected variability gene
    expression and influence to results of Differential Expression analysis.
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: 7.2.3
Config/testthat/edition: 3
BugReports: https://github.com/baerlachlan/darr/issues
URL: https://github.com/baerlachlan/darr
BiocType: Software
biocViews: Sequencing, RNASeq, SNP, GenomicVariation, VariantAnnotation,
    DifferentialExpression
VignetteBuilder: knitr
Depends: 
    GenomicRanges,
    ggplot2,
    R (>= 4.3.0)
Imports: 
    BiocGenerics,
    GenomeInfoDb,
    Gviz,
    IRanges,
    MatrixGenerics,
    methods,
    rlang,
    Rsamtools,
    S4Vectors,
    stats,
    VariantAnnotation
Suggests: 
    BiocStyle,
    covr,
    knitr,
    limma,
    rmarkdown,
    testthat (>= 3.0.0),
    tidyverse

[vjcitn]

Hi, thanks for your submission. I have to request that you consider a different name for your package. There is already one called dar in the pipeline. Something more expressive like DiffAllelicRep would probably be good for user comprehension. Once a package is in the system, changing names is cumbersome, so we want to preempt this concern. Let me know your thoughts.

[baerlachlan]

Hi @vjcitn, thanks for spotting this. Unfortunate timing. I didn't think of recently submitted packages when checking for name clashes. Would there be any issues if we change the name to "tadar" as an acronym for Transcriptome Analysis of Differential Allelic Representation?

[lshep]

I think that would be better yes. Please resubmit with tadar. Thank you.