CNVRanger
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see CNVRanger.
Summarization and expression/phenotype association of CNV ranges
Bioconductor version: 3.9
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 sph.cuny.edu>
citation("CNVRanger")):
Installation
To install this package, start R (version "3.6") 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 | 1.0.3 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5 years) |
| License | Artistic-2.0 |
| Depends | GenomicRanges, RaggedExperiment |
| Imports | BiocParallel, GDSArray, GenomeInfoDb, Gviz, 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, MultiAssayExperiment, TCGAutils, curatedTCGAData, ensembldb, knitr, regioneR, rmarkdown |
| 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_1.0.3.tar.gz |
| Windows Binary | CNVRanger_1.0.3.zip |
| Mac OS X 10.11 (El Capitan) | CNVRanger_1.0.3.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 |
| Old Source Packages for BioC 3.9 | Source Archive |