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ACE

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing


Bioconductor version: Release (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

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