CNVRanger

This is the development version of CNVRanger; for the stable release version, see CNVRanger.

Summarization and expression/phenotype association of CNV ranges

Bioconductor version: Development (3.19)

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 gmail.com>

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

Installation

To install this package, start R (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software
Version	1.19.1
In Bioconductor since	BioC 3.9 (R-3.6) (5 years)
License	Artistic-2.0
Depends	GenomicRanges, RaggedExperiment
Imports	BiocGenerics, 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

Suggests	AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, TxDb.Hsapiens.UCSC.hg19.knownGene, curatedTCGAData, ensembldb, grid, knitr, org.Hs.eg.db, regioneR, rmarkdown, statmod
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	CNVRanger_1.19.1.tar.gz
Windows Binary	CNVRanger_1.19.1.zip (64-bit only)
macOS Binary (x86_64)	CNVRanger_1.19.1.tgz
macOS Binary (arm64)
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