Package: sesame 1.25.2
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.
Authors:
sesame_1.25.2.tar.gz
sesame_1.25.1.zip(r-4.5)sesame_1.25.1.zip(r-4.4)sesame_1.25.0.zip(r-4.3)
sesame_1.25.2.tgz(r-4.4-any)sesame_1.25.0.tgz(r-4.3-any)
sesame_1.25.2.tar.gz(r-4.5-noble)sesame_1.25.2.tar.gz(r-4.4-noble)
sesame_1.25.2.tgz(r-4.4-emscripten)sesame_1.25.0.tgz(r-4.3-emscripten)
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-1.25.1(bioc 3.21)sesame-1.24.0(bioc 3.20)
dnamethylationmethylationarraypreprocessingqualitycontrolbioinformaticsdna-methylationmicroarray
Last updated 2 days agofrom:9791ef76ef. Checks:ERROR: 4 WARNING: 3. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | FAIL | Dec 22 2024 |
R-4.5-win | WARNING | Dec 04 2024 |
R-4.5-linux | ERROR | Dec 22 2024 |
R-4.4-win | WARNING | Dec 04 2024 |
R-4.4-mac | WARNING | Dec 22 2024 |
R-4.3-win | ERROR | Dec 01 2024 |
R-4.3-mac | ERROR | Dec 01 2024 |
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