AneuFinder

This package is for version 3.14 of Bioconductor; for the stable, up-to-date release version, see AneuFinder.

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


Bioconductor version: 3.14

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 "4.1") 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 1.22.0
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, ReorderCluster, mclust
System Requirements
URL https://github.com/ataudt/aneufinder.git
See More
Suggests knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package AneuFinder_1.22.0.tar.gz
Windows Binary AneuFinder_1.22.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra) AneuFinder_1.22.0.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
Old Source Packages for BioC 3.14 Source Archive