ACE

DOI: 10.18129/B9.bioc.ACE  

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Bioconductor version: Release (3.16)

Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.

Author: Jos B Poell

Maintainer: Jos B Poell <j.poell at amsterdamumc.nl>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("ACE")

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("ACE")

 

HTML	R Script	ACE vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, Coverage, DNASeq, Sequencing, Software, Visualization, WholeGenome
Version	1.16.0
In Bioconductor since	BioC 3.8 (R-3.5) (4.5 years)
License	GPL-2
Depends	R (>= 3.4)
Imports	Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle
SystemRequirements
Enhances
URL	https://github.com/tgac-vumc/ACE
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ACE_1.16.0.tar.gz
Windows Binary	ACE_1.16.0.zip
macOS Binary (x86_64)	ACE_1.16.0.tgz
macOS Binary (arm64)	ACE_1.16.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ACE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ACE
Bioc Package Browser	https://code.bioconductor.org/browse/ACE/
Package Short Url	https://bioconductor.org/packages/ACE/
Package Downloads Report	Download Stats