ACE

DOI: 10.18129/B9.bioc.ACE    

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Bioconductor version: Release (3.8)

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>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ACE", version = "3.8")

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 1.0.0
License GPL-2
Depends R (>= 3.4)
Imports Biobase, QDNAseq, ggplot2, grid, stats, utils, methods, grDevices
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_1.0.0.tar.gz
Windows Binary ACE_1.0.0.zip
Mac OS X 10.11 (El Capitan) ACE_1.0.0.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 http://bioconductor.org/packages/ACE/
Package Downloads Report Download Stats

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