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Infer locally aneuploid cells using single cell RNA-seq data

Bioconductor version: Release (3.19)

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")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

partCNV_vignette HTML R Script
Reference Manual PDF


biocViews Classification, CopyNumberVariation, HiddenMarkovModel, SingleCell, Software
Version 1.2.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License GPL-2
Depends R (>= 3.5.0)
Imports stats, data.table, depmixS4, Seurat, SingleCellExperiment, AnnotationHub, magrittr, GenomicRanges
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Suggests BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package partCNV_1.2.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) partCNV_1.2.0.tgz
macOS Binary (arm64) partCNV_1.2.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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