AneuFinder

DOI: 10.18129/B9.bioc.AneuFinder    

This is the development version of AneuFinder; for the stable release version, see AneuFinder.

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

Bioconductor version: Development (3.11)

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>

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

Installation

To install this package, start R (version "4.0") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 1.15.0
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, BiocGenerics(>= 0.31.6), 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_1.15.0.tar.gz
Windows Binary AneuFinder_1.15.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) AneuFinder_1.15.0.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

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