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 (3.20)
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 "4.4") 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 | 1.21.0 |
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_1.21.0.tar.gz |
Windows Binary | CNVRanger_1.21.0.zip |
macOS Binary (x86_64) | CNVRanger_1.21.0.tgz |
macOS Binary (arm64) | CNVRanger_1.21.0.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 |