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conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Bioconductor version: Release (3.17)

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

Author: Volker Hovestadt, Marc Zapatka

Maintainer: Volker Hovestadt <conumee at hovestadt.bio>

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

Installation

To install this package, start R (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("conumee")

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("conumee")
conumee HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, QualityControl, Software
Version 1.34.0
In Bioconductor since BioC 3.1 (R-3.2) (8.5 years)
License GPL (>= 2)
Depends R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest
Imports methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, GenomeInfoDb
Linking To
Suggests BiocStyle, knitr, rmarkdown, minfiData, RCurl
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me CopyNeutralIMA
Links To Me
Build Report  

Package Archives

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

Source Package conumee_1.34.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64) conumee_1.34.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/conumee
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/conumee
Bioc Package Browser https://code.bioconductor.org/browse/conumee/
Package Short Url https://bioconductor.org/packages/conumee/
Package Downloads Report Download Stats