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
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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-1.23.0(bioc 3.21)CNVRanger-1.22.0(bioc 3.20)

copynumbervariation differentialexpression geneexpression genomewideassociation genomicvariation microarray rnaseq snp bioconductor-package

5.87 score 7 stars 9 scripts 212 downloads 1 mentions 10 exports 65 dependencies

Last updated 2 months agofrom:7cbb1a6e9a. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:cnvEQTL cnvGWAS cnvOncoPrint generateGDS importLrrBaf plotEQTL plotManhattan plotRecurrentRegions populationRanges setupCnvGWAS

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocParallel Biostrings calibrate cli codetools cpp11 crayon curl data.table DelayedArray edgeR formatR futile.logger futile.options GDSArray gdsfmt generics GenomeInfoDb GenomeInfoDbData GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mime openssl plyr qqman R6 RaggedExperiment rappdirs Rcpp reshape2 rlang S4Arrays S4Vectors SeqArray snow SNPRelate SparseArray statmod stringi stringr SummarizedExperiment sys UCSC.utils vctrs XVector zlibbioc

Summarization and quantitative trait analysis of CNV ranges

Vinicius Henrique da Silva, Ludwig Geistlinger

Rendered fromCNVRanger.Rmdusingknitr::rmarkdownon Nov 29 2024.

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

Citation

Development and contributors

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