Package: MinimumDistance
Title: A Package for De Novo CNV Detection in Case-Parent Trios
Version: 1.54.0
Date: 2025-07-24
Author: Robert B Scharpf and Ingo Ruczinski
Authors@R: person("Robert", "Scharpf", email="rscharpf@jhu.edu", role=c("aut", "cre"))
Description: Analysis of de novo copy number variants in trios from
        high-dimensional genotyping platforms.
License: Artistic-2.0
Depends: R (>= 3.5.0), VanillaICE (>= 1.47.1)
Imports: methods, BiocGenerics, MatrixGenerics, Biobase, S4Vectors (>=
        0.23.18), IRanges, Seqinfo, GenomicRanges (>= 1.17.16),
        SummarizedExperiment (>= 1.15.4), oligoClasses, DNAcopy, ff,
        foreach, matrixStats, lattice, data.table, grid, stats, utils
Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18,
        BSgenome.Hsapiens.UCSC.hg19, RUnit
Collate: 'help.R' 'AllClasses.R' 'AllGenerics.R' 'coercion-methods.R'
        'datasets.R' 'defunct.R' 'functions.R' 'generator-funs.R'
        'lattice-methods.R' 'mad-methods.R'
        'methods-AnnotatedDataFrame.R' 'methods-AssayData.R'
        'methods-FileViews.R' 'methods-FilterParamMD.R'
        'methods-ILimit.R' 'methods-MDRanges.R'
        'methods-MinDistExperiment.R' 'methods-MinDistGRanges.R'
        'methods-MinDistParam.R' 'methods-MinDistPosterior.R'
        'methods-ParentOffspring.R' 'methods-ParentOffspringList.R'
        'methods-Pedigree.R' 'methods-PennParam.R'
        'methods-ShallowSimpleList.R' 'methods-SummarizedExperiment.R'
        'methods-TrioSet.R' 'methods-TrioSetList.R'
        'methods-ff_array.R' 'methods-grid.R' 'methods-list.R'
        'methods-matrix.R' 'segment2-methods.R' 'utils.R' 'zzz.R'
Enhances: snow, doSNOW
LazyLoad: yes
biocViews: Microarray, SNP, CopyNumberVariation
RoxygenNote: 7.1.1
Encoding: UTF-8
Config/pak/sysreqs: make libbz2-dev liblzma-dev libxml2-dev libssl-dev
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:10:57 UTC
RemoteUrl: https://github.com/bioc/MinimumDistance
RemoteRef: RELEASE_3_22
RemoteSha: ac79af776bf37a33c2ef69865ada5c17aaaf4db1
NeedsCompilation: no
Packaged: 2025-11-11 21:06:45 UTC; root
Maintainer: Robert Scharpf <rscharpf@jhu.edu>
Built: R 4.5.2; ; 2025-11-11 21:13:24 UTC; windows
