DOI: 10.18129/B9.bioc.partCNV  

Infer locally aneuploid cells using single cell RNA-seq data

Bioconductor version: Release (3.18)

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).

Author: Ziyi Li [aut, cre, ctb], Ruoxing Li [ctb]

Maintainer: Ziyi Li <zli16 at>

Citation (from within R, enter citation("partCNV")):


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biocViews Classification, CopyNumberVariation, HiddenMarkovModel, SingleCell, Software
Version 1.0.0
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
License GPL-2
Depends R (>= 3.5.0)
Imports stats, data.table, depmixS4, Seurat, SingleCellExperiment, AnnotationHub, magrittr, GenomicRanges
Suggests BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
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Source Package partCNV_1.0.0.tar.gz
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macOS Binary (x86_64) partCNV_1.0.0.tgz
macOS Binary (arm64) partCNV_1.0.0.tgz
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