DESCRIPTION

Package: CNVWorkshop
Version: 1.0.0
Title: Copy number variation analysis with Bioconductor 
Author: Ludwig Geistlinger, Marcel Ramos, Sehyun Oh, Levi Waldron
Maintainer: Ludwig Geistlinger <ludwig_geistlinger@hms.harvard.edu>
Description: This workshop gives an overview of Bioconductor solutions for the
    analysis of copy number variation (CNV) data. The workshop introduces Bioconductor 
    core data structures for efficient representation, access, and manipulation of
    CNV data, and how to use these containers for structured downstream analysis of
    CNVs and integration with gene expression and quantitative phenotypes. 
    Participants will be provided with code and hands-on practice for a comprehensive
    set of typical analysis steps including exploratory analysis, summarizing 
    individual CNV calls across a population, overlap analysis with functional 
    genomic regions and regulatory elements, expression quantitative trait loci 
    (eQTL) analysis, and genome-wide association analysis (GWAS) with quantitative 
    phenotypes. As an advanced application example, the workshop also introduces
    allele-specific absolute copy number analysis and how it is incorporated in 
    cancer genomic analysis for the estimation of tumor characteristics such as 
    tumor purity and ploidy.
Depends: 
    CNVRanger,
    PureCN,
    RaggedExperiment,
    regioneR
Imports:
    MultiAssayExperiment,
    SummarizedExperiment,
    TCGAutils,
    curatedTCGAData,
    ensembldb,
    statmod
Suggests:
    AnnotationHub,
    BSgenome.Btaurus.UCSC.bosTau6.masked, 
    ComplexHeatmap,
    Gviz,
    TxDb.Hsapiens.UCSC.hg19.knownGene,
    knitr,
    org.Hs.eg.db,
    pkgdown,
    rmarkdown
License: Artistic-2.0
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
biocViews: 
    CopyNumberVariation,
    DifferentialExpression,
    GeneExpression,
    GenomeWideAssociation,
    GenomicVariation,
    Microarray, 
    RNASeq,
    SNP 
RoxygenNote: 6.1.1
URL: https://waldronlab.github.io/CNVWorkshop
DockerImage: ludwigg/cnvworkshop:latest