Package: partCNV
Type: Package
Title: Infer locally aneuploid cells using single cell RNA-seq data
Version: 1.0.0
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
Suggests: BiocStyle, 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
git_url: https://git.bioconductor.org/packages/partCNV
git_branch: RELEASE_3_18
git_last_commit: 4075147
git_last_commit_date: 2023-10-24
Date/Publication: 2023-10-24
NeedsCompilation: no
Packaged: 2023-10-24 22:24:38 UTC; biocbuild
Author: Ziyi Li [aut, cre, ctb],
  Ruoxing Li [ctb]
Maintainer: Ziyi Li <zli16@mdanderson.org>
Depends: R (>= 3.5.0)
Built: R 4.3.2; ; 2023-12-06 23:24:47 UTC; unix
