partCNV
This package is for version 3.23 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see partCNV.
Infer locally aneuploid cells using single cell RNA-seq data
Bioconductor version: Release (3.23)
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("partCNV")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Classification, CopyNumberVariation, HiddenMarkovModel, SingleCell, Software |
| Version | 1.9.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-2 |
| Depends | R (>= 3.5.0) |
| Imports | stats, data.table, depmixS4, Seurat, SingleCellExperiment, AnnotationHub, magrittr, GenomicRanges, BiocStyle |
| System Requirements | |
| URL |
See More
| Suggests | rmarkdown, knitr, IRanges, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | partCNV_1.9.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-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 |