ACE

This is the development version of ACE; for the stable release version, see ACE.

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Bioconductor version: Development (3.21)

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>

Citation (from within R, enter citation("ACE")):

Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

ACE vignette	HTML	R Script
Reference Manual	PDF
NEWS	Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, Coverage, DNASeq, Sequencing, Software, Visualization, WholeGenome
Version	1.25.0
In Bioconductor since	BioC 3.8 (R-3.5) (6 years)
License	GPL-2
Depends	R (>= 3.4)
Imports	Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices, GenomicRanges
System Requirements
URL	https://github.com/tgac-vumc/ACE

Suggests	knitr, rmarkdown, BiocStyle
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	ACE_1.25.0.tar.gz
Windows Binary (x86_64)
macOS Binary (x86_64)
macOS Binary (arm64)
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