CNVRanger
Summarization and expression/phenotype association of CNV ranges
Bioconductor version: 3.24 · Package version: 1.29.4
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software |
| Package Short Url | https://bioconductor.org/packages/CNVRanger/ |
Citation
From within R, enter citation("CNVRanger"):
Ludwig Geistlinger, Vinicius Henrique da Silva. CNVRanger: Summarization and expression/phenotype association of CNV ranges. doi:10.18129/B9.bioc.CNVRanger, R package version 1.29.4, https://bioconductor.org/packages/CNVRanger.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | CNVRanger_1.29.4.tar.gz |
| Windows binary (x86_64) | CNVRanger_1.29.4.zip |
| macOS binary (arm64) | CNVRanger_1.29.4.tgz |
| macOS binary (x86_64) | CNVRanger_1.29.4.tgz |
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