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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 mdanderson.org>

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

Installation

To install this package, start R (version "4.3") and enter:


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

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")
partCNV_vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

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
System Requirements
URL
See More
Suggests BiocStyle, rmarkdown, knitr, IRanges, testthat (>= 3.0.0)
Linking To
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Depends On Me
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Package Archives

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

Source Package partCNV_1.0.0.tar.gz
Windows Binary partCNV_1.0.0.zip
macOS Binary (x86_64) partCNV_1.0.0.tgz
macOS Binary (arm64) partCNV_1.0.0.tgz
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