CNVRanger
This is thereleased version of CNVRanger; for the devel version, seeCNVRanger.
Summarization and expression/phenotype association of CNV ranges
Bioconductor version: Release (3.22)
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]
ORCID: 0000-0002-2495-5464, Vinicius Henrique da Silva [aut], Marcel Ramos [ctb] ORCID: 0000-0002-3242-0582, Levi Waldron [ctb] ORCID: 0000-0003-2725-0694
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")BiocManager::install("CNVRanger")For older versions of R, please refer to the appropriateBioconductor 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 | 1.26.0 |
| In Bioconductor since | BioC 3.9 (R-3.6) (6.5 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
FollowInstallation instructions to use this package in your R session.
| Source Package | CNVRanger_1.26.0.tar.gz |
| Windows Binary (x86_64) | CNVRanger_1.26.0.zip |
| macOS Binary (x86_64) | CNVRanger_1.26.0.tgz |
| macOS Binary (arm64) | CNVRanger_1.26.0.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 |