Package: lumi 2.57.0
lumi: BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.
Authors:
lumi_2.57.0.tar.gz
lumi_2.57.0.zip(r-4.5)lumi_2.57.0.zip(r-4.4)lumi_2.57.0.zip(r-4.3)
lumi_2.57.0.tgz(r-4.4-any)lumi_2.57.0.tgz(r-4.3-any)
lumi_2.57.0.tar.gz(r-4.5-noble)lumi_2.57.0.tar.gz(r-4.4-noble)
lumi_2.57.0.tgz(r-4.4-emscripten)lumi_2.57.0.tgz(r-4.3-emscripten)
lumi.pdf |lumi.html✨
lumi/json (API)
NEWS
# Install 'lumi' in R: |
install.packages('lumi', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- example.lumi - Example Illumina Expression data in LumiBatch class
- example.lumiMethy - Example Illumina Infinium Methylation data in MethyLumiM class
- example.methyTitration - Example Illumina Infinium Methylation titration data in MethyLumiM class
On BioConductor:lumi-2.57.0(bioc 3.20)lumi-2.56.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:2833a3e4f7
Exports:addAnnotationInfoaddControlData2lumiaddControlData2methyLumiMaddNuId2lumiaddNuID2lumiadjColorBias.quantileadjColorBias.ssnasBigMatrixbeadNumbeadNum<-beta2mbgAdjustbgAdjustMethylationboxplotboxplotColorBiascoercecolorBiasSummarycombinecontrolDatacontrolData<-densitydetectiondetection<-detectionCalldetectOutlierestimateBetaestimateIntensityestimateLumiCVestimateMestimateMethylationBGexprsexprs<-gammaFitEMgetChipInfogetChrInfogetControlDatagetControlProbegetControlTypegetHistorygetNuIDMappingInfohistid2seqIlluminaID2nuIDimportMethyIDATinverseVSTis.nuIDlumiBlumiExpressolumiMethyBlumiMethyClumiMethyNlumiMethyRlumiMethyStatuslumiNlumiQlumiRlumiR.batchlumiTm2betaMAplotmethylationCallnormalizeMethylation.quantilenormalizeMethylation.ssnnuID2EntrezIDnuID2IlluminaIDnuID2probeIDnuID2RefSeqIDnuID2targetIDpairsplotplotCDFplotColorBias1DplotColorBias2DplotControlDataplotDensityplotGammaFitplotHousekeepingGeneplotSampleRelationplotStringencyGeneplotVSTprobeID2nuIDproduceGEOPlatformFileproduceGEOSampleInfoTemplateproduceGEOSubmissionFileproduceMethylationGEOSubmissionFilerankinvariantrsnsampleNames<-se.exprsse.exprs<-seq2idshowsmoothQuantileNormalizationssnsummarytargetID2nuIDvst
Dependencies:abindaffyaffyioannotateAnnotationDbiaskpassbase64beanplotBHBiobaseBiocGenericsBiocIOBiocManagerBiocParallelBiostringsbitbit64bitopsblobbumphuntercachemclicliprcodetoolscolorspacecpp11crayoncurldata.tableDBIDelayedArrayDelayedMatrixStatsdigestdoRNGdplyrfansifarverfastmapFDb.InfiniumMethylation.hg19foreachformatRfutile.loggerfutile.optionsgenefiltergenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesGEOqueryggplot2gluegtableHDF5ArrayhmshttrilluminaioIRangesisobanditeratorsjsonliteKEGGRESTKernSmoothlabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmclustmemoisemethylumimgcvmimeminfimulttestmunsellnleqslvnlmenor1mixopensslorg.Hs.eg.dbpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrquadprogR.methodsS3R.ooR.utilsR6RColorBrewerRcppRCurlreadrreshapereshape2restfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrngtoolsRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalesscrimesiggenessnowSparseArraysparseMatrixStatsstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectTxDb.Hsapiens.UCSC.hg19.knownGenetzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXMLxml2xtableXVectoryamlzlibbioc