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AneuFinder

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


Bioconductor version: Release (3.18)

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 "4.3") 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")
A quick introduction to AneuFinder PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome
Version 1.30.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
URL https://github.com/ataudt/aneufinder.git
See More
Suggests knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
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Build Report Build Report

Package Archives

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

Source Package AneuFinder_1.30.0.tar.gz
Windows Binary AneuFinder_1.30.0.zip (64-bit only)
macOS Binary (x86_64) AneuFinder_1.30.0.tgz
macOS Binary (arm64) AneuFinder_1.30.0.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