Package: AllelicImbalance
Type: Package
Title: Investigates Allele Specific Expression
Version: 1.49.0
Date: 2021-11-17
Encoding: UTF-8
Author: Jesper R Gadin, Lasse Folkersen
Maintainer: Jesper R Gadin <j.r.gadin@gmail.com>
Description: Provides a framework for allelic specific expression
    investigation using RNA-seq data.
License: GPL-3
URL: https://github.com/pappewaio/AllelicImbalance
BugReports: https://github.com/pappewaio/AllelicImbalance/issues
Suggests:
    testthat,
    org.Hs.eg.db,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    SNPlocs.Hsapiens.dbSNP144.GRCh37,
    BiocStyle,
    knitr,
    rmarkdown
Depends:
    R (>= 4.0.0),
    grid,
    GenomicRanges (>= 1.31.8),
    SummarizedExperiment (>= 0.2.0),
    GenomicAlignments (>= 1.15.6)
Imports:
    methods,
    BiocGenerics,
    AnnotationDbi,
    BSgenome (>= 1.47.3),
    VariantAnnotation (>= 1.25.11),
    Biostrings (>= 2.47.6),
    S4Vectors (>= 0.17.25),
    IRanges (>= 2.13.12),
    Rsamtools (>= 1.99.3),
    GenomicFeatures (>= 1.31.3),
    Gviz,
    lattice,
    latticeExtra,
    gridExtra,
    seqinr,
    GenomeInfoDb,
    nlme
LazyData: TRUE
biocViews: Genetics, Infrastructure, Sequencing
VignetteBuilder: knitr
Collate:
    'AllelicImbalance-package.R'
    'initialize-methods.R'
    'ASEset-class.R'
    'DetectedAI-class.R'
    'GlobalAnalysis-class.R'
    'barplot-methods.R'
    'locationplot-methods.R'
    'GvizTrack-methods.R'
    'LinkVariantAlmlof-class.R'
    'RegionSummary-class.R'
    'RiskVariant-class.R'
    'auxillary-functions-annotation.R'
    'auxillary-functions-visuals.R'
    'auxillary-methods-annotation.R'
    'auxillary-methods-summaries.R'
    'auxillary-methods.R'
    'chisq.test-methods.R'
    'binom.test-methods.R'
    'boxplot-methods.R'
    'deprecations.R'
    'detect-methods.R'
    'filter-methods.R'
    'histplot-methods.R'
    'inference-methods.R'
    'linkage-methods.R'
    'list-methods.R'
    'mapbias-methods.R'
    'plot-methods.R'
    'show-methods.R'
    'simulation-methods.R'
    'summary-methods.R'
    'utils.R'
RoxygenNote: 7.1.1
git_url: https://git.bioconductor.org/packages/AllelicImbalance
git_branch: devel
git_last_commit: d78bb64
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
