Package: CNVRanger 1.23.0
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_1.23.0.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')) |
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
Last updated 23 days agofrom:7cbb1a6e9a. Checks:OK: 1 NOTE: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 30 2024 |
R-4.5-win | NOTE | Oct 30 2024 |
R-4.5-linux | NOTE | Oct 30 2024 |
R-4.4-win | NOTE | Oct 30 2024 |
R-4.4-mac | NOTE | Oct 30 2024 |
R-4.3-win | NOTE | Oct 30 2024 |
R-4.3-mac | NOTE | Oct 30 2024 |
Exports:cnvEQTLcnvGWAScnvOncoPrintgenerateGDSimportLrrBafplotEQTLplotManhattanplotRecurrentRegionspopulationRangessetupCnvGWAS
Dependencies:abindaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocParallelBiostringscalibrateclicodetoolscpp11crayoncurldata.tableDelayedArrayedgeRformatRfutile.loggerfutile.optionsGDSArraygdsfmtGenomeInfoDbGenomeInfoDbDataGenomicRangesgluehttrIRangesjsonlitelambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmimeopensslplyrqqmanR6RaggedExperimentrappdirsRcppreshape2rlangS4ArraysS4VectorsSeqArraysnowSNPRelateSparseArraystatmodstringistringrSummarizedExperimentsysUCSC.utilsvctrsXVectorzlibbioc
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 |