ACE

DOI: 10.18129/B9.bioc.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 (3.11)

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 "4.0") and enter:

if (!requireNamespace("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")

 

HTML R Script ACE vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews CopyNumberVariation, Coverage, DNASeq, Sequencing, Software, Visualization, WholeGenome
Version 1.5.0
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_1.5.0.tar.gz
Windows Binary ACE_1.5.0.zip
Mac OS X 10.11 (El Capitan) ACE_1.5.0.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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: