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CNVRanger

Summarization and expression/phenotype association of CNV ranges


Bioconductor version: Release (3.18)

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 1.18.1
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
See More
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
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Package Archives

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

Source Package CNVRanger_1.18.1.tar.gz
Windows Binary CNVRanger_1.18.1.zip
macOS Binary (x86_64) CNVRanger_1.18.1.tgz
macOS Binary (arm64) CNVRanger_1.18.0.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 3.18 Source Archive