AneuFinder (original) (raw)
This is the released version of AneuFinder; for the devel version, seeAneuFinder.
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Bioconductor version: Release (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")Details
| biocViews | CopyNumberVariation, GenomicVariation, HiddenMarkovModel, ImmunoOncology, Sequencing, SingleCell, Software, WholeGenome |
|---|---|
| Version | 1.34.0 |
| In Bioconductor since | BioC 3.3 (R-3.3) (8.5 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, 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_1.34.0.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/ |
| Package Downloads Report | Download Stats |