conumee

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Bioconductor version: 3.23 · Package version: 1.46.0

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

Installation

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

BiocManager::install("conumee")

Details

Maintainer	Volker Hovestadt <conumee@hovestadt.bio>
Author	Volker Hovestadt, Marc Zapatka
License	GPL (>= 2)
Downloads rank	654
Source branch	RELEASE_3_23
biocViews	CopyNumberVariation, DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, QualityControl, Software

Documentation

The conumee vignette

Download

Follow the installation instructions to use this package in your R session.

Source package	conumee_1.46.0.tar.gz
Windows binary (x86_64)	conumee_1.46.0.zip
macOS binary (arm64)	conumee_1.46.0.tgz
macOS binary (x86_64)	conumee_1.46.0.tgz

Dependencies

Depends: R (>= 3.5.0), minfi, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylation450kmanifest, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest

Imports: methods, stats, DNAcopy, rtracklayer, GenomicRanges, IRanges, Seqinfo

Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl

Reverse dependencies

Suggests Me (1): CopyNeutralIMA