AneuFinder

DOI: 10.18129/B9.bioc.AneuFinder  

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Bioconductor version: Release (3.17)

AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.

Author: Aaron Taudt, Bjorn Bakker, David Porubsky

Maintainer: Aaron Taudt <aaron.taudt at gmail.com>

Installation

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

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

BiocManager::install("AneuFinder")

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("AneuFinder")

 

PDF	R Script	A quick introduction to AneuFinder
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome
Version	1.28.0
In Bioconductor since	BioC 3.3 (R-3.3) (7.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData
Imports	methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics(>= 0.31.6), S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, mclust
LinkingTo
Suggests	knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
SystemRequirements
Enhances
URL	https://github.com/ataudt/aneufinder.git
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	AneuFinder_1.28.0.tar.gz
Windows Binary	AneuFinder_1.28.0.zip (64-bit only)
macOS Binary (x86_64)	AneuFinder_1.28.0.tgz
macOS Binary (arm64)	AneuFinder_1.28.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AneuFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AneuFinder
Bioc Package Browser	https://code.bioconductor.org/browse/AneuFinder/
Package Short Url	https://bioconductor.org/packages/AneuFinder/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.17	Source Archive