AneuFinder
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see AneuFinder.
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Bioconductor version: 3.9
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("AneuFinder")):
Installation
To install this package, start R (version "3.6") 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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome |
| Version | 1.12.1 |
| 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, 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_1.12.1.tar.gz |
| Windows Binary | AneuFinder_1.12.1.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | AneuFinder_1.12.1.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 3.9 | Source Archive |