AneuFinder

DOI: 10.18129/B9.bioc.AneuFinder    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see AneuFinder.

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

Bioconductor version: 3.9

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 "3.6") and enter:

if (!requireNamespace("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	1.12.1
In Bioconductor since	BioC 3.3 (R-3.3) (3.5 years)
License	Artistic-2.0
Depends	R (>= 3.5), GenomicRanges, ggplot2, cowplot, AneuFinderData
Imports	methods, utils, grDevices, graphics, stats, foreach, doParallel, S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, ecp, Biostrings, GenomicAlignments, reshape2, ggdendro, ggrepel, ReorderCluster, 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_1.12.1.tar.gz
Windows Binary	AneuFinder_1.12.1.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	AneuFinder_1.12.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AneuFinder
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/AneuFinder
Package Short Url	https://bioconductor.org/packages/AneuFinder/
Package Downloads Report	Download Stats