Package: PureCN
Type: Package
Title: Copy number calling and SNV classification using targeted short
        read sequencing
Version: 2.16.0
Date: 2025-07-22
Authors@R: c(person("Markus", "Riester",
                    role = c("aut", "cre"),
                    email = "markus.riester@novartis.com",
                    comment = c(ORCID = "0000-0002-4759-8332")),
             person("Angad P.", "Singh", role = "aut"))
Description: This package estimates tumor purity, copy number, and loss
        of heterozygosity (LOH), and classifies single nucleotide
        variants (SNVs) by somatic status and clonality. PureCN is
        designed for targeted short read sequencing data, integrates
        well with standard somatic variant detection and copy number
        pipelines, and has support for tumor samples without matching
        normal samples.
Depends: R (>= 3.5.0), DNAcopy, VariantAnnotation (>= 1.14.1)
Imports: GenomicRanges (>= 1.20.3), IRanges (>= 2.2.1), RColorBrewer,
        S4Vectors, data.table, grDevices, graphics, stats, utils,
        SummarizedExperiment, Seqinfo, GenomeInfoDb, GenomicFeatures,
        Rsamtools, Biobase, Biostrings, BiocGenerics, rtracklayer,
        ggplot2, gridExtra, futile.logger, VGAM, tools, methods,
        mclust, rhdf5, Matrix
Suggests: BiocParallel, BiocStyle, PSCBS, R.utils,
        TxDb.Hsapiens.UCSC.hg19.knownGene, covr, knitr, optparse,
        org.Hs.eg.db, jsonlite, markdown, rmarkdown, testthat
Enhances: genomicsdb (>= 0.0.3)
VignetteBuilder: knitr
License: Artistic-2.0
BugReports: https://github.com/lima1/PureCN/issues
URL: https://github.com/lima1/PureCN
biocViews: CopyNumberVariation, Software, Sequencing,
        VariantAnnotation, VariantDetection, Coverage, ImmunoOncology
NeedsCompilation: no
ByteCompile: yes
RoxygenNote: 7.3.1
Config/pak/sysreqs: make libbz2-dev liblzma-dev libpng-dev libxml2-dev
        libssl-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:31:57 UTC
RemoteUrl: https://github.com/bioc/PureCN
RemoteRef: RELEASE_3_22
RemoteSha: c7ace8b15abb55d8f28ea09069143c08772c2ed7
Packaged: 2025-11-11 16:51:31 UTC; root
Author: Markus Riester [aut, cre] (ORCID:
    <https://orcid.org/0000-0002-4759-8332>),
  Angad P. Singh [aut]
Maintainer: Markus Riester <markus.riester@novartis.com>
Built: R 4.5.2; ; 2025-11-11 17:02:12 UTC; windows
