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Bioconductor - CNVRanger (development version)

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 (3.22)

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: 0000-0002-2495-5464 , Vinicius Henrique da Silva [aut], Marcel Ramos [ctb] ORCID: 0000-0002-3242-0582 , Levi Waldron [ctb] 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")

# 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 Details biocViews CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software Version 1.25.4 In Bioconductor since BioC 3.9 (R-3.6) (6 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 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.

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