Package: CNVRanger 1.29.1
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:
CNVRanger_1.29.1.tar.gz
CNVRanger_1.29.1.zip(r-4.7)CNVRanger_1.29.1.zip(r-4.6)CNVRanger_1.29.1.zip(r-4.5)
CNVRanger_1.29.1.tgz(r-4.6-any)CNVRanger_1.29.1.tgz(r-4.5-any)
CNVRanger_1.29.1.tar.gz(r-4.7-any)CNVRanger_1.29.1.tar.gz(r-4.6-any)
CNVRanger_1.29.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CNVRanger/json (API)
| # Install 'CNVRanger' in R: |
| install.packages('CNVRanger', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/cnvranger/issues
On BioConductor:CNVRanger-1.29.1(bioc 3.24)CNVRanger-1.28.0(bioc 3.23)
copynumbervariationdifferentialexpressiongeneexpressiongenomewideassociationgenomicvariationmicroarrayrnaseqsnpbioconductor-packageu24ca289073
Last updated from:53d628f90b. Checks:1 NOTE, 8 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 349 | ||
| linux-devel-x86_64 | ERROR | 459 | ||
| source / vignettes | ERROR | 478 | ||
| linux-release-x86_64 | ERROR | 468 | ||
| macos-release-arm64 | ERROR | 212 | ||
| macos-oldrel-arm64 | ERROR | 290 | ||
| windows-devel | ERROR | 1103 | ||
| windows-release | ERROR | 1058 | ||
| windows-oldrel | ERROR | 1056 | ||
| wasm-release | OK | 260 |
Exports:cnvEQTLcnvGWAScnvOncoPrintgenerateGDSimportLrrBafplotEQTLplotManhattanplotRecurrentRegionspopulationRangessetupCnvGWAS
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelBiostringscalibrateclicodetoolscpp11crayoncurldata.tableDelayedArraydigestedgeRformatRfutile.loggerfutile.optionsGDSArraygdsfmtgenericsGenomeInfoDbGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslplyrqqmanR6RaggedExperimentrappdirsRcppreshape2RhpcBLASctlrlangS4ArraysS4VectorsSeqArraySeqinfosnowSNPRelateSparseArraystatmodstringistringrSummarizedExperimentsysUCSC.utilsvctrsXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| CNV-expression association analysis | cnvEQTL |
| Run the CNV-GWAS | cnvGWAS |
| OncoPrint plot for CNV regions | cnvOncoPrint |
| Produce CNV-GDS for the phenotyped samples | generateGDS |
| Import LRR and BAF from text files used in the CNV analysis | importLrrBaf |
| Plot EQTL region | plotEQTL |
| Manhattan Plot | plotManhattan |
| Plot recurrent CNV regions | plotRecurrentRegions |
| Summarizing CNV ranges across a population | populationRanges |
| Setup the folders and files to run CNV-GWAS analysis | setupCnvGWAS |
