Package: scquantum
Title: Estimate Ploidy and Absolute Copy Number from Single Cell
        Sequencing
Version: 1.0.0
Authors@R: c(
    person(given = "Alexander",
           family = "Davis",
           role = c("aut", "cre"),
           email = "alexlovesmolecules@gmail.com"),
    person(given = "Taylor",
           family = "Arnold",
           role = "cph",
           comment = "Author of segmentation function"),
    person(given = "Veeranjaneyulu",
           family = "Sadhanala",
           role = "cph",
           comment = "Author of segmentation function"),
    person(given = "Ryan",
           family = "Tibshirani",
           role = "cph",
           comment = "Author of segmentation function"))
Description: Given bincount data from single-cell copy number profiling
        (segmented or unsegmented), estimates ploidy, and uses the
        ploidy estimate to scale the data to absolute copy numbers.
        Uses the modular quantogram proposed by Kendall (1986)
        <doi:10.1002/0471667196.ess2129.pub2>, modified by weighting
        segments according to confidence, and quantifying confidence in
        the estimate using a theoretical quantogram. Includes optional
        fused-lasso segmentation with the algorithm in Johnson (2013)
        <doi:10.1080/10618600.2012.681238>, using the implementation
        from glmgen by Arnold, Sadhanala, and Tibshirani.
License: GPL (>= 2)
Encoding: UTF-8
RoxygenNote: 7.1.2
Suggests: testthat (>= 3.0.0)
Config/testthat/edition: 3
NeedsCompilation: yes
Packaged: 2026-10-20 10:02:50 UTC; root
Author: Alexander Davis [aut, cre], Taylor Arnold [cph] (Author of
        segmentation function), Veeranjaneyulu Sadhanala [cph] (Author
        of segmentation function), Ryan Tibshirani [cph] (Author of
        segmentation function)
Maintainer: Alexander Davis <alexlovesmolecules@gmail.com>
Repository: https://alex-l-m.r-universe.dev
Date/Publication: 2022-03-23 08:00:06 UTC
RemoteUrl: https://github.com/cran/scquantum
RemoteRef: HEAD
RemoteSha: b6fcd39eeffd807e2a89587fd391b0d5e58af196