CNVRanger

DOI: 10.18129/B9.bioc.CNVRanger    

This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see CNVRanger.

Summarization and expression/phenotype association of CNV ranges

Bioconductor version: 3.15

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 hms.harvard.edu>

Installation

To install this package, start R (version "4.2") 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")

 

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

Details

biocViews	CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software
Version	1.12.0
In Bioconductor since	BioC 3.9 (R-3.6) (3.5 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
LinkingTo
Suggests	AnnotationHub, BSgenome.Btaurus.UCSC.bosTau6.masked, BiocStyle, ComplexHeatmap, Gviz, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, grid, knitr, regioneR, rmarkdown
SystemRequirements
Enhances
URL
BugReports	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_1.12.0.tar.gz
Windows Binary	CNVRanger_1.12.0.zip
macOS Binary (x86_64)	CNVRanger_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/CNVRanger
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/CNVRanger
Package Short Url	https://bioconductor.org/packages/CNVRanger/
Package Downloads Report	Download Stats