partCNV

DOI: 10.18129/B9.bioc.partCNV  

This is the development version of partCNV; for the stable release version, see partCNV.

Infer locally aneuploid cells using single cell RNA-seq data

Bioconductor version: Development (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 mdanderson.org>

Installation

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

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("partCNV")

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

Documentation

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

browseVignettes("partCNV")

 

HTML	R Script	partCNV_vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	Classification, CopyNumberVariation, HiddenMarkovModel, SingleCell, Software
Version	1.1.0
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
LinkingTo
Suggests	BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	partCNV_1.1.0.tar.gz
Windows Binary	partCNV_1.1.0.zip
macOS Binary (x86_64)	partCNV_1.1.0.tgz
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/partCNV
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/partCNV
Bioc Package Browser	https://code.bioconductor.org/browse/partCNV/
Package Short Url	https://bioconductor.org/packages/partCNV/
Package Downloads Report	Download Stats