conumee

This is the released version of conumee; for the devel version, see conumee.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Bioconductor version: Release (3.23)

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")):

Volker Hovestadt, Marc Zapatka. conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays. doi:10.18129/B9.bioc.conumee, R package version 1.46.0, https://bioconductor.org/packages/conumee.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, QualityControl, Software
Version	1.46.0
In Bioconductor since	BioC 3.1 (R-3.2) (11.5 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, Seqinfo
System Requirements
URL

Suggests	BiocStyle, knitr, rmarkdown, minfiData, RCurl
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me	CopyNeutralIMA
Links To Me
Build Report	Build Report, r-universe

Package Archives

Follow 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 (big-sur-x86_64)	conumee_1.46.0.tgz
macOS Binary (sonoma-arm64)	conumee_1.46.0.tgz
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