Package: conumee 1.41.0

Volker Hovestadt

conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays

This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.

Authors:Volker Hovestadt, Marc Zapatka

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conumee.pdf |conumee.html✨
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NEWS

# Install 'conumee' in R:

install.packages('conumee', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

detail_regions - Detail_regions
exclude_regions - Exclude_regions
tcgaBRCA.sentrix2name - TcgaBRCA.sentrix2name

On BioConductor:conumee-1.41.0(bioc 3.21)conumee-1.40.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

copynumbervariation dnamethylation methylationarray microarray normalization preprocessing qualitycontrol software

5.48 score 30 scripts 438 downloads 25 mentions 13 exports 140 dependencies

Last updated 5 months agofrom:f47752d891. Checks:1 OK, 8 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 29 2025
R-4.5-win	NOTE	Mar 29 2025
R-4.5-mac	NOTE	Mar 29 2025
R-4.5-linux	NOTE	Mar 29 2025
R-4.4-win	NOTE	Mar 29 2025
R-4.4-mac	NOTE	Mar 29 2025
R-4.4-linux	NOTE	Mar 29 2025
R-4.3-win	NOTE	Mar 29 2025
R-4.3-mac	NOTE	Dec 29 2024

Exports:CNV.bin CNV.create_anno CNV.detail CNV.detailplot CNV.detailplot_wrap CNV.fit CNV.genomeplot CNV.load CNV.process CNV.segment CNV.write read.450k.url show

Dependencies:abind annotate AnnotationDbi askpass base64 beanplot BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cli clipr codetools cpp11 crayon curl data.table DBI DelayedArray DelayedMatrixStats digest DNAcopy doRNG dplyr fansi fastmap foreach formatR futile.logger futile.options genefilter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GEOquery glue h5mread HDF5Array hms httr httr2 IlluminaHumanMethylation450kanno.ilmn12.hg19 IlluminaHumanMethylation450kmanifest IlluminaHumanMethylationEPICanno.ilm10b2.hg19 IlluminaHumanMethylationEPICmanifest illuminaio IRanges iterators jsonlite KEGGREST lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust memoise mime minfi multtest nlme nor1mix openssl pillar pkgconfig plogr plyr png preprocessCore prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RColorBrewer Rcpp RCurl readr rentrez reshape restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rngtools Rsamtools RSQLite rtracklayer rvest S4Arrays S4Vectors scrime selectr siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs vroom withr XML xml2 xtable XVector yaml

The conumee vignette

Volker Hovestadt, Marc Zapatka (Division of Molecular Genetics, German Cancer Research Center, Heidelberg, Germany)

Rendered fromconumee.Rmdusingknitr::rmarkdownon Mar 29 2025.

Last update: 2017-04-13
Started: 2015-04-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
CNV.analysis class	CNV.analysis-class coef,CNV.analysis-method names,CNV.analysis-method names<-,CNV.analysis-method show,CNV.analysis-method
CNV.anno class	CNV.anno-class show,CNV.anno-method
CNV.bin	CNV.bin CNV.bin,CNV.analysis-method
CNV.check	CNV.check CNV.check,CNV.data-method
CNV.create_anno	CNV.create_anno
CNV.create_bins	CNV.create_bins
CNV.data class	CNV.data-class names,CNV.data-method names<-,CNV.data-method show,CNV.data-method [,CNV.data,ANY,ANY,ANY-method
CNV.detail	CNV.detail CNV.detail,CNV.analysis-method
CNV.detailplot	CNV.detailplot CNV.detailplot,CNV.analysis-method
CNV.detailplot_wrap	CNV.detailplot_wrap CNV.detailplot_wrap,CNV.analysis-method
CNV.fit	CNV.fit CNV.fit,CNV.data,CNV.data,CNV.anno-method
CNV.genomeplot	CNV.genomeplot CNV.genomeplot,CNV.analysis-method
CNV.load	CNV.load CNV.load,data.frame-method CNV.load,GenomicRatioSet-method CNV.load,matrix-method CNV.load,MethylSet-method CNV.load,numeric-method
CNV.merge_bins	CNV.merge_bins
CNV.process	CNV.process CNV.process,integer,integer,CNV.data,CNV.anno-method
CNV.segment	CNV.segment CNV.segment,CNV.analysis-method
CNV.write	CNV.write CNV.write,CNV.analysis-method
detail_regions	detail_regions
exclude_regions	exclude_regions
read.450k.url	read.450k.url
tbl_ucsc	tbl_ucsc
tcgaBRCA.sentrix2name	tcgaBRCA.sentrix2name