conumee

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see conumee.

Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Bioconductor version: 3.18

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, DNAMethylation, MethylationArray, Microarray, Normalization, Preprocessing, QualityControl, Software

Version 1.36.0

In Bioconductor since BioC 3.1 (R-3.2) (9 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

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

Package Archives

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

Source Package conumee_1.36.0.tar.gz

Windows Binary

macOS Binary (x86_64) conumee_1.36.0.tgz

macOS Binary (arm64) conumee_1.36.0.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/

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