conumee

DOI: 10.18129/B9.bioc.conumee    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see conumee.

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Bioconductor version: 3.15

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>

Installation

To install this package, start R (version "4.2") 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")

 

HTML	R Script	conumee
PDF		Reference Manual
Text		NEWS

Details

biocViews	CopyNumberVariation, DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, QualityControl, Software
Version	1.30.0
In Bioconductor since	BioC 3.1 (R-3.2) (7.5 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
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, minfiData, RCurl
SystemRequirements
Enhances
URL
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_1.30.0.tar.gz
Windows Binary
macOS Binary (x86_64)
Source Repository	git clone https://git.bioconductor.org/packages/conumee
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/conumee
Package Short Url	https://bioconductor.org/packages/conumee/
Package Downloads Report	Download Stats