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: 2022-03-16 17:28:46 UTC; alexdavis
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: CRAN
Date/Publication: 2022-03-23 09:00:06 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-04-25 22:11:56 UTC; unix
Archs: scquantum.so.dSYM
