Package: conumee 1.47.1

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

conumee_1.47.1.tar.gz
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conumee_1.47.1.tgz(r-4.6-any)conumee_1.47.1.tgz(r-4.5-any)
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conumee_1.47.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
conumee/json (API)

# 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-1.47.1(bioc 3.24)conumee-1.46.0(bioc 3.23)

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

5.92 score 42 scripts 25 mentions 13 exports 143 dependencies

Last updated from:afd7c582f8. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	580
linux-devel-x86_64	NOTE	1462
source / vignettes	OK	906
linux-release-x86_64	NOTE	1516
macos-release-arm64	NOTE	996
macos-oldrel-arm64	NOTE	1147
windows-devel	NOTE	1564
windows-release	NOTE	1483
windows-oldrel	NOTE	1467
wasm-release	OK	500

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 BiocBaseUtils BiocFileCache BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob bumphunter cachem cigarillo cli clipr codetools cpp11 crayon curl data.table DBI dbplyr DelayedArray DelayedMatrixStats digest dir.expiry DNAcopy doRNG dplyr fastmap filelock foreach formatR futile.logger futile.options genefilter generics 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 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 Seqinfo siggenes snow SparseArray sparseMatrixStats statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tzdb utf8 vctrs vroom withr XML xml2 xtable XVector yaml

The conumee vignette

Rendered fromconumee.Rmdusingknitr::rmarkdown

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