CNVRanger

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see CNVRanger.

Summarization and expression/phenotype association of CNV ranges


Bioconductor version: 3.10

The CNVRanger package implements a comprehensive tool suite for CNV analysis. This includes functionality for summarizing individual CNV calls across a population, assessing overlap with functional genomic regions, and association analysis with gene expression and quantitative phenotypes.

Author: Ludwig Geistlinger [aut, cre], Vinicius Henrique da Silva [aut], Marcel Ramos [ctb], Levi Waldron [ctb]

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at sph.cuny.edu>

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

Installation

To install this package, start R (version "3.6") and enter:


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

BiocManager::install("CNVRanger")

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("CNVRanger")
Summarization and quantitative trait analysis of CNV ranges HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software
Version 1.2.2
In Bioconductor since BioC 3.9 (R-3.6) (5 years)
License Artistic-2.0
Depends GenomicRanges, RaggedExperiment
Imports BiocParallel, GDSArray, GenomeInfoDb, IRanges, S4Vectors, SNPRelate, SummarizedExperiment, data.table, edgeR, gdsfmt, grDevices, lattice, limma, methods, plyr, qqman, rappdirs, reshape2, stats, utils
System Requirements
URL
Bug Reports https://github.com/waldronlab/CNVRanger/issues
See More
Suggests AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, Gviz, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, knitr, regioneR, rmarkdown
Linking To
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Build Report Build Report

Package Archives

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

Source Package CNVRanger_1.2.2.tar.gz
Windows Binary CNVRanger_1.2.2.zip
Mac OS X 10.11 (El Capitan) CNVRanger_1.2.2.tgz
Source Repository git clone https://git.bioconductor.org/packages/CNVRanger
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CNVRanger
Bioc Package Browser https://code.bioconductor.org/browse/CNVRanger/
Package Short Url https://bioconductor.org/packages/CNVRanger/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.10 Source Archive