Package: conumee 1.39.0

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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NEWS

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

Peer review:

Datasets:

On BioConductor:conumee-1.39.0(bioc 3.20)conumee-1.38.0(bioc 3.19)

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

bioconductor-package

13 exports 0.82 score 135 dependencies 25 mentions

Last updated 2 months agofrom:07777b1ce1

Exports:CNV.binCNV.create_annoCNV.detailCNV.detailplotCNV.detailplot_wrapCNV.fitCNV.genomeplotCNV.loadCNV.processCNV.segmentCNV.writeread.450k.urlshow

Dependencies:abindannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestDNAcopydoRNGdplyrfansifastmapforeachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryglueHDF5ArrayhmshttrIlluminaHumanMethylation450kanno.ilmn12.hg19IlluminaHumanMethylation450kmanifestIlluminaHumanMethylationEPICanno.ilm10b2.hg19IlluminaHumanMethylationEPICmanifestilluminaioIRangesiteratorsjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemimeminfimulttestnlmenor1mixopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreadrreshaperestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscrimesiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsvroomwithrXMLxml2xtableXVectoryamlzlibbioc

The conumee vignette

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

Rendered fromconumee.Rmdusingknitr::rmarkdownon Jun 24 2024.

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

Readme and manuals

Help Manual

Help pageTopics
CNV.analysis classCNV.analysis-class coef,CNV.analysis-method names,CNV.analysis-method names<-,CNV.analysis-method show,CNV.analysis-method
CNV.anno classCNV.anno-class show,CNV.anno-method
CNV.binCNV.bin CNV.bin,CNV.analysis-method
CNV.checkCNV.check CNV.check,CNV.data-method
CNV.create_annoCNV.create_anno
CNV.create_binsCNV.create_bins
CNV.data classCNV.data-class names,CNV.data-method names<-,CNV.data-method show,CNV.data-method [,CNV.data,ANY,ANY,ANY-method
CNV.detailCNV.detail CNV.detail,CNV.analysis-method
CNV.detailplotCNV.detailplot CNV.detailplot,CNV.analysis-method
CNV.detailplot_wrapCNV.detailplot_wrap CNV.detailplot_wrap,CNV.analysis-method
CNV.fitCNV.fit CNV.fit,CNV.data,CNV.data,CNV.anno-method
CNV.genomeplotCNV.genomeplot CNV.genomeplot,CNV.analysis-method
CNV.loadCNV.load CNV.load,data.frame-method CNV.load,GenomicRatioSet-method CNV.load,matrix-method CNV.load,MethylSet-method CNV.load,numeric-method
CNV.merge_binsCNV.merge_bins
CNV.processCNV.process CNV.process,integer,integer,CNV.data,CNV.anno-method
CNV.segmentCNV.segment CNV.segment,CNV.analysis-method
CNV.writeCNV.write CNV.write,CNV.analysis-method
detail_regionsdetail_regions
exclude_regionsexclude_regions
read.450k.urlread.450k.url
tbl_ucsctbl_ucsc
tcgaBRCA.sentrix2nametcgaBRCA.sentrix2name