Package: CNVRanger 1.23.0

Ludwig Geistlinger

CNVRanger: Summarization and expression/phenotype association of CNV ranges

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.

Authors:Ludwig Geistlinger [aut, cre], Vinicius Henrique da Silva [aut], Marcel Ramos [ctb], Levi Waldron [ctb]

CNVRanger_1.23.0.tar.gz
CNVRanger_1.23.0.zip(r-4.5)CNVRanger_1.23.0.zip(r-4.4)CNVRanger_1.23.0.zip(r-4.3)
CNVRanger_1.23.0.tgz(r-4.4-any)CNVRanger_1.23.0.tgz(r-4.3-any)
CNVRanger_1.23.0.tar.gz(r-4.5-noble)CNVRanger_1.23.0.tar.gz(r-4.4-noble)
CNVRanger_1.23.0.tgz(r-4.4-emscripten)CNVRanger_1.23.0.tgz(r-4.3-emscripten)
CNVRanger.pdf |CNVRanger.html
CNVRanger/json (API)
NEWS

# Install 'CNVRanger' in R:
install.packages('CNVRanger', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/waldronlab/cnvranger/issues

On BioConductor:CNVRanger-1.21.0(bioc 3.20)CNVRanger-1.20.0(bioc 3.19)

copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnpbioconductor-package

5.87 score 7 stars 9 scripts 206 downloads 10 exports 64 dependencies

Last updated 23 days agofrom:7cbb1a6e9a. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:cnvEQTLcnvGWAScnvOncoPrintgenerateGDSimportLrrBafplotEQTLplotManhattanplotRecurrentRegionspopulationRangessetupCnvGWAS

Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelBiostringscalibrateclicodetoolscpp11crayoncurldata.tableDelayedArrayedgeRformatRfutile.loggerfutile.optionsGDSArraygdsfmtGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslplyrqqmanR6RaggedExperimentrappdirsRcppreshape2rlangS4ArraysS4VectorsSeqArraysnowSNPRelateSparseArraystatmodstringistringrSummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc

Summarization and quantitative trait analysis of CNV ranges

Rendered fromCNVRanger.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-07-30
Started: 2018-10-17