Package: partCNV
Type: Package
Title: Infer locally aneuploid cells using single cell RNA-seq data
Version: 1.8.0
Authors@R: c(
	person(given="Ziyi", family="Li", email="zli16@mdanderson.org", role=c("aut", "cre", "ctb")),
	person(given="Ruoxing", family="Li", email="ruoxingli@outlook.com", role="ctb"))
Description: This package uses a statistical framework for rapid and
        accurate detection of aneuploid cells with local copy number
        deletion or amplification. Our method uses an EM algorithm with
        mixtures of Poisson distributions while incorporating
        cytogenetics information (e.g., regional deletion or
        amplification) to guide the classification (partCNV). When
        applicable, we further improve the accuracy by integrating a
        Hidden Markov Model for feature selection (partCNVH).
Imports: stats, data.table, depmixS4, Seurat, SingleCellExperiment,
        AnnotationHub, magrittr, GenomicRanges, BiocStyle
Suggests: rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
Dependents: R (>= 4.2.0)
VignetteBuilder: knitr
License: GPL-2
Encoding: UTF-8
RoxygenNote: 7.2.3
biocViews: Software, CopyNumberVariation, HiddenMarkovModel,
        SingleCell, Classification
Config/testthat/edition: 3
Config/pak/sysreqs: libglpk-dev make libicu-dev libpng-dev libxml2-dev
        libssl-dev python3 zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 15:23:33 UTC
RemoteUrl: https://github.com/bioc/partCNV
RemoteRef: RELEASE_3_22
RemoteSha: d29e8a01cd10c26a53feb3cec51167adbafa9e40
NeedsCompilation: no
Packaged: 2025-11-11 16:37:15 UTC; root
Author: Ziyi Li [aut, cre, ctb],
  Ruoxing Li [ctb]
Maintainer: Ziyi Li <zli16@mdanderson.org>
Depends: R (>= 3.5.0)
Built: R 4.5.2; ; 2025-11-11 16:41:55 UTC; windows
