Package: M3Drop 1.31.0
M3Drop: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.
Authors:
M3Drop_1.31.0.tar.gz
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M3Drop.pdf |M3Drop.html✨
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NEWS
# Install 'M3Drop' in R: |
install.packages('M3Drop', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/tallulandrews/m3drop/issues
On BioConductor:M3Drop-1.31.0(bioc 3.20)M3Drop-1.30.0(bioc 3.19)
Last updated 2 months agofrom:65bab9cacf
Exports:BrenneckeGetVariableGenesConsensus_FScorFSginiFSirlbaPcaFSM3DropCleanDataM3DropConvertDataM3DropDropoutModelsM3DropExpressionHeatmapM3DropFeatureSelectionM3DropGetExtremesM3DropGetHeatmapClustersM3DropGetHeatmapNamesM3DropGetMarkersM3DropSimulationTrifectaM3DropTestShiftM3DropThreeSetVennNBumiCheckFitNBumiCheckFitFSNBumiCoexpressionNBumiCompareModelsNBumiConvertDataNBumiConvertToIntegerNBumiFeatureSelectionCombinedDropNBumiFeatureSelectionHighVarNBumiFitBasicModelNBumiFitDispVsMeanNBumiFitModelNBumiHVGNBumiImputeNormNBumiPearsonResidualsNBumiPearsonResidualsApproxNBumiSimulationTrifectaPoissonUMIFeatureSelectionDropouts
Dependencies:abindaskpassbackportsbase64encbbmlebdsmatrixbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbslibcachemCairocallrcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArrayDelayedMatrixStatsdensEstBayesdescdigestdistributionaldqrngevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegplotsgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrinlineIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecycleloomagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetnumDerivopensslpheatmappillarpkgbuildpkgconfigpngposteriorprocessxpsQuickJSRR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppHNSWRcppMLRcppParallelRcppProgressreldistrlangrmarkdownrpartRSpectrarstanrstantoolsrstudioapirsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscuttleSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsStanHeadersstatmodstringistringrSummarizedExperimentsyssystemfontstensorAtextshapingtibbletinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXVectoryamlzlibbioc