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>
Citation (from within R, enter
citation("ACE")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, Coverage, DNASeq, Sequencing, Software, Visualization, WholeGenome |
| Version | 1.2.0 |
| 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 |
See More
| Suggests | knitr, rmarkdown, BiocStyle |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | 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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/ACE/ |
| Package Short Url | https://bioconductor.org/packages/ACE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |