CNVRanger

Summarization and expression/phenotype association of CNV ranges

Bioconductor version: 3.23 · Package version: 1.28.0

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.

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("CNVRanger")

Details

Maintainer	Ludwig Geistlinger <ludwig.geistlinger@gmail.com>
Author	Ludwig Geistlinger [aut, cre] (ORCID: <https://orcid.org/0000-0002-2495-5464>), Vinicius Henrique da Silva [aut], Marcel Ramos [ctb] (ORCID: <https://orcid.org/0000-0002-3242-0582>), Levi Waldron [ctb] (ORCID: <https://orcid.org/0000-0003-2725-0694>)
License	Artistic-2.0
Bug Reports	https://github.com/waldronlab/CNVRanger/issues
Downloads rank	354
Source branch	RELEASE_3_23
biocViews	CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software

Documentation

Summarization and quantitative trait analysis of CNV ranges

Download

Source package

Dependencies

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

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