AneuFinder

This package is for version 3.20 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see AneuFinder.

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

DOI: 10.18129/B9.bioc.AneuFinder

Bioconductor version: 3.20

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 "4.4") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome

Version 1.34.0

In Bioconductor since BioC 3.3 (R-3.3) (9 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

Suggests knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10

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Package Archives

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

Source Package AneuFinder_1.34.0.tar.gz

Windows Binary (x86_64) AneuFinder_1.34.0.zip (64-bit only)

macOS Binary (x86_64) AneuFinder_1.34.0.tgz

macOS Binary (arm64) AneuFinder_1.34.0.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/

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