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ACE

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see ACE.

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing


Bioconductor version: 3.18

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 "4.3") 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")
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 1.20.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
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Suggests knitr, rmarkdown, BiocStyle
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Package Archives

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

Source Package ACE_1.20.0.tar.gz
Windows Binary ACE_1.20.0.zip
macOS Binary (x86_64) ACE_1.20.0.tgz
macOS Binary (arm64) ACE_1.20.0.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