DESCRIPTION

Package: trellis
Title: Somatic structural variant analysis
Version: 1.0.1
Author: Rob Scharpf, Daniel Bruhm, Dorothy Hallberg, Victor Velculescu
Maintainer: Rob Scharpf <rscharpf@jhu.edu>
Description: Analysis of somatic structural variants from whole genome sequencing.
Depends:
    R (>= 4.0.0),
    GenomicRanges
Imports:
    methods,
    BiocGenerics,
    S4Vectors,
    Rsamtools,
    GenomeInfoDb,
    GenomicAlignments (>= 1.10.0),
    IRanges,
    SummarizedExperiment,
    graph,
    stats,
    DNAcopy,
    matrixStats,
    utils,
    dplyr (>= 0.8.5),
    tidyr,
    RBGL,
    magrittr,
    ggplot2,
    RColorBrewer,
    AnnotationDbi,
    scales,
    GenomicFeatures,
    BSgenome,
    Biostrings,
    grid,
    gridExtra,
    tibble,
    purrr,
    readr
Suggests:
    tidyverse,
    knitr,
    testthat,
    svbams,
    BSgenome.Hsapiens.UCSC.hg19,
    TxDb.Hsapiens.UCSC.hg19.refGene,
    svfilters.hg18,
    svfilters.hg19,
    BiocStyle,
    rmarkdown,
    data.table,
    org.Hs.eg.db,
    ggnet,
    network,
    sna,
    Rgraphviz,
    kableExtra
Collate: 
    'help.R'
    'AllGenerics.R'
    'Amplicon-class.R'
    'DNAcopy-class.R'
    'GAlignmentPairs-utils.R'
    'Rearrangement-class.R'
    'Deletion-class.R'
    'DeletionList-class.R'
    'DeletionParam-class.R'
    'ExonSubset-class.R'
    'GRanges-utils.R'
    'Preprocess-class.R'
    'RearrangementList-class.R'
    'RearrangementParams-class.R'
    'RearrangmentParams-class.R'
    'SegmentParam-class.R'
    'Transcripts-class.R'
    'acf.R'
    'alignment-utils.R'
    'amplicon-utils.R'
    'baf-utils.R'
    'blat-utils.R'
    'copynumber-methods.R'
    'data-utils.R'
    'data.R'
    'deletion-utils.R'
    'fasta-utils.R'
    'functions.R'
    'functions_for_CRAM.R'
    'fusion-utils.R'
    'galignment-utils.R'
    'germlineOutliers.R'
    'improper-methods.R'
    'listCNVs.R'
    'listGenomeFilters.R'
    'preprocess-utils.R'
    'read_pairs.R'
    'rear_reads.R'
    'rearrangement-utils.R'
    'rearlist-utils.R'
    'recurrent.R'
    'segment.R'
    'seqinfo-utils.R'
    'uniprot.R'
LazyData: true
VignetteBuilder: knitr
biocViews: Sequencing, HighThroughputSequencing, CopyNumberVariants
Encoding: UTF-8
RoxygenNote: 7.3.2
License: GPL-3