CNVRanger

This is the released version of CNVRanger; for the devel version, see CNVRanger.

Summarization and expression/phenotype association of CNV ranges

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DOI: 10.18129/B9.bioc.CNVRanger

Bioconductor version: Release (3.22)

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] ORCID iD ORCID: 0000-0002-2495-5464 , Vinicius Henrique da Silva [aut], Marcel Ramos [ctb] ORCID iD ORCID: 0000-0002-3242-0582 , Levi Waldron [ctb] ORCID iD ORCID: 0000-0003-2725-0694

Maintainer: Ludwig Geistlinger <ludwig.geistlinger at gmail.com>

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

Installation

To install this package, start R (version "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software

Version 1.26.0

In Bioconductor since BioC 3.9 (R-3.6) (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

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Package Archives

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

Source Package CNVRanger_1.26.0.tar.gz

Windows Binary (x86_64) CNVRanger_1.26.0.zip (64-bit only)

macOS Binary (x86_64) CNVRanger_1.26.0.tgz

macOS Binary (arm64) CNVRanger_1.26.0.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/

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