bamSliceR: Slicing and Tallied BAMs from GDC and local for Variants Analysis

[huangyizR]

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• Repository: https://github.com/trichelab/bamSliceR

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[bioc-issue-bot]

Hi @huangyizR

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: bamSliceR
Type: Package
Title: Slicing and Tallied BAMs from GDC and local for Variants Analysis
Version: 0.99.0
Authors@R: c( 
        person("Peter", "Huang", role=c("aut", "cre"), 
      email="peterhuang319@gmail.com",
      comment=c(ORCID="0009-0004-5689-0193")),
        person("Lauren", "Harmon", role=c("ctb"),
      email="Lauren.Harmon@vai.org",
      comment=c(ORCID="0000-0002-2248-060")), 
        person("Timothy", "Triche", role=c("ctb"),
      comment=c(ORCID="0000-0001-5665-946X")))
Description: A standardized pipeline for extracting, annotating, and analyzing genomic variants across large controlled-access repositories.
Depends: R (> 4.0), 
         gmapR,
         VariantAnnotation,
         GenomicRanges,
         plyranges,
         GenomicDataCommons, 
         Rsamtools,
         rtracklayer
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
VignetteBuilder: knitr
biocViews: DataImport, Sequencing
Suggests: 
    knitr,
    rmarkdown,
    pkgdown
Imports: 
    BiocParallel,
    biomaRt,
    Homo.sapiens,
    httr,
    jsonlite,
    stringr,
    BSgenome.Hsapiens.UCSC.hg38,
    TxDb.Hsapiens.UCSC.hg38.knownGene,
    VariantTools,
    data.table,
    maftools, 
    RColorBrewer,
    IRanges,
    S4Vectors,
    methods