CNVRanger
This is the released version of CNVRanger; for the devel version, see CNVRanger.
Summarization and expression/phenotype association of CNV ranges
Bioconductor version: Release (3.23)
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 gmail.com>
citation("CNVRanger")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software |
| Version | 1.28.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (7.5 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 |
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.
| Source Package | CNVRanger_1.28.0.tar.gz |
| Windows Binary (x86_64) | CNVRanger_1.28.0.zip |
| macOS Binary (big-sur-x86_64) | CNVRanger_1.28.0.tgz |
| macOS Binary (sonoma-arm64) | CNVRanger_1.28.0.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/ |
| Package Downloads Report | Download Stats |