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 (3.21)
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")):
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 | ||
| NEWS | Text |
Details
| biocViews | CopyNumberVariation, DifferentialExpression, GeneExpression, GenomeWideAssociation, GenomicVariation, Microarray, RNASeq, SNP, Software |
| Version | 1.23.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (5.5 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_1.23.0.tar.gz |
| Windows Binary (x86_64) | CNVRanger_1.23.0.zip |
| macOS Binary (x86_64) | CNVRanger_1.23.0.tgz |
| macOS Binary (arm64) | |
| 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 |