Package: sesame 1.25.3
sesame: SEnsible Step-wise Analysis of DNA MEthylation BeadChips
Tools For analyzing Illumina Infinium DNA methylation arrays. SeSAMe provides utilities to support analyses of multiple generations of Infinium DNA methylation BeadChips, including preprocessing, quality control, visualization and inference. SeSAMe features accurate detection calling, intelligent inference of ethnicity, sex and advanced quality control routines.
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sesame_1.25.3.tar.gz
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sesame.pdf |sesame.html✨
sesame/json (API)
NEWS
# Install 'sesame' in R: |
install.packages('sesame', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zwdzwd/sesame/issues
On BioConductor:sesame-1.25.3(bioc 3.21)sesame-1.24.0(bioc 3.20)
dnamethylationmethylationarraypreprocessingqualitycontrolbioinformaticsdna-methylationmicroarray
Last updated 3 months agofrom:715da261c4. Checks:3 ERROR, 4 WARNING. Indexed: yes.
Target | Result | Latest binary |
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Doc / Vignettes | FAIL | Mar 06 2025 |
R-4.5-win | WARNING | Mar 06 2025 |
R-4.5-mac | WARNING | Mar 06 2025 |
R-4.5-linux | ERROR | Mar 06 2025 |
R-4.4-win | WARNING | Mar 06 2025 |
R-4.4-mac | WARNING | Mar 06 2025 |
R-4.4-linux | ERROR | Mar 06 2025 |
Exports:addMaskbetasCollapseToPfxBetaValueToMValuebisConversionControlcalcEffectSizecheckLevelscnSegmentationcompareMouseStrainReferencecompareMouseTissueReferencecompareReferencecontrolscreateUCSCtrackdeIdentifydetectionPnegEcdfdiffRefSetdmContrastsDMLDMLpredictDMRdyeBiasCorrdyeBiasCorrMostBalanceddyeBiasCorrTypeINormdyeBiasLdyeBiasNLELBARestimateLeukocyteformatVCFgetAFsgetAFTypeIbySumAllelesgetBetasgetMaskgetRefSetimputeBetasimputeBetasByGenomicNeighborsimputeBetasMatrixByMeaninferEthnicityinferInfiniumIChannelinferSexinferSpeciesinferStraininferTissueinitFileSetliftOverlistAvailableMasksmapFileSetmapToMammal40matchDesignmeanIntensitymedianTotalIntensitymLiftOverMValueToBetaValuenoMaskednoobopenSesameopenSesameToFilepalgenparseGEOsignalMUpOOBAHpredictAgepredictAgeHorvath353predictAgeSkinBloodpredictMouseAgeInMonthprefixMaskprefixMaskButCprefixMaskButCGprepSesameprepSesameListprobeID_designTypeprobeSuccessRatequalityMaskreadFileSetreadIDATpairrecommendedMaskNamesreIdentifyresetMaskscrubscrubSoftsdf_read_tablesdf_write_tablesdfPlatformsearchIDATprefixessesame_checkVersionsesameAnno_attachManifestsesameAnno_buildAddressFilesesameAnno_buildManifestGRangessesameAnno_downloadsesameAnno_readManifestTSVsesameQC_calcStatssesameQC_getStatssesameQC_plotBarsesameQC_plotBetaByDesignsesameQC_plotHeatSNPssesameQC_plotIntensVsBetassesameQC_plotRedGrnQQsesameQC_rankStatssesameQCtoDFsesamizesetMaskSigDFsignalMUsliceFileSetsummaryExtractTesttotalIntensitiesupdateSigDFvisualizeGenevisualizeProbesvisualizeRegionvisualizeSegments
Dependencies:abindAnnotationDbiAnnotationHubaskpassBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobcachemclicliprcodetoolscolorspacecpp11crayoncurlDBIdbplyrDelayedArraydplyrExperimentHubfansifarverfastmapfilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegtablehmshttrIRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplyrpngpreprocessCoreprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrreshape2rlangRSQLiteS4ArraysS4VectorsscalessesameDatasnowSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwheatmapwithrXVectoryaml