CNVRanger

Summarization and expression/phenotype association of CNV ranges

Bioconductor version: Release (3.17)

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 "4.3") 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	1.16.5
In Bioconductor since	BioC 3.9 (R-3.6) (4.5 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
Linking To
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
System Requirements
Enhances
URL
Bug Reports	https://github.com/waldronlab/CNVRanger/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	CNVRanger_1.16.5.tar.gz
Windows Binary	CNVRanger_1.16.5.zip
macOS Binary (x86_64)	CNVRanger_1.16.5.tgz
macOS Binary (arm64)	CNVRanger_1.16.5.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 3.17	Source Archive