AneuFinder

DOI: 10.18129/B9.bioc.AneuFinder    

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

Bioconductor version: Release (3.6)

This package implements functions for CNV calling, plotting, export and analysis from whole-genome single cell sequencing data.

Author: Aaron Taudt, Bjorn Bakker, David Porubsky

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("AneuFinder")

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, Software, WholeGenome
Version	1.6.0
In Bioconductor since	BioC 3.3 (R-3.3) (2 years)
License	Artistic-2.0
Depends	R (>= 3.3), GenomicRanges, cowplot, AneuFinderData
Imports	methods, utils, grDevices, graphics, stats, foreach, doParallel, BiocGenerics, S4Vectors, GenomeInfoDb, IRanges, Rsamtools, bamsignals, DNAcopy, Biostrings, GenomicAlignments, ggplot2, 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
Build Report

Package Archives

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

Source Package	AneuFinder_1.6.0.tar.gz
Windows Binary	AneuFinder_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	AneuFinder_1.6.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/AneuFinder
Package Short Url	http://bioconductor.org/packages/AneuFinder/
Package Downloads Report	Download Stats