ACE

DOI: 10.18129/B9.bioc.ACE    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ACE.

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Bioconductor version: 3.9

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 vumc.nl>

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("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	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
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_1.2.0.tar.gz
Windows Binary	ACE_1.2.0.zip
Mac OS X 10.11 (El Capitan)	ACE_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ACE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ACE
Package Short Url	https://bioconductor.org/packages/ACE/
Package Downloads Report	Download Stats