Package: M3Drop 1.33.0
Tallulah Andrews
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_1.33.0.tar.gz
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M3Drop.pdf |M3Drop.html✨
M3Drop/json (API)
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-1.33.0(bioc 3.21)M3Drop-1.32.0(bioc 3.20)
rnaseqsequencingtranscriptomicsgeneexpressionsoftwaredifferentialexpressiondimensionreductionfeatureextractionhuman-cell-atlasrna-seqsingle-cellsingle-cell-rna-seq
Last updated 23 days agofrom:a036ab73d8. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 18 2024 |
| R-4.5-win | NOTE | Nov 18 2024 |
| R-4.5-linux | NOTE | Nov 18 2024 |
| R-4.4-win | NOTE | Nov 18 2024 |
| R-4.4-mac | NOTE | Nov 18 2024 |
| R-4.3-win | NOTE | Nov 18 2024 |
| R-4.3-mac | NOTE | Nov 18 2024 |
Exports:BrenneckeGetVariableGenesConsensus_FScorFSginiFSirlbaPcaFSM3DropCleanDataM3DropConvertDataM3DropDropoutModelsM3DropExpressionHeatmapM3DropFeatureSelectionM3DropGetExtremesM3DropGetHeatmapClustersM3DropGetHeatmapNamesM3DropGetMarkersM3DropSimulationTrifectaM3DropTestShiftM3DropThreeSetVennNBumiCheckFitNBumiCheckFitFSNBumiCoexpressionNBumiCompareModelsNBumiConvertDataNBumiConvertToIntegerNBumiFeatureSelectionCombinedDropNBumiFeatureSelectionHighVarNBumiFitBasicModelNBumiFitDispVsMeanNBumiFitModelNBumiHVGNBumiImputeNormNBumiPearsonResidualsNBumiPearsonResidualsApproxNBumiSimulationTrifectaPoissonUMIFeatureSelectionDropouts
Dependencies:abindaskpassassortheadbackportsbase64encbbmlebdsmatrixbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsbslibcachemCairocallrcaToolscheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydensEstBayesdescdigestdistributionaldqrngevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegplotsgridExtragtablegtoolshighrHmischtmlTablehtmltoolshtmlwidgetshttrinlineIRangesirlbaisobandjquerylibjsonliteKernSmoothknitrlabelinglambda.rlatticelifecycleloomagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellmvtnormnlmennetnumDerivopensslpheatmappillarpkgbuildpkgconfigpngposteriorprocessxpsQuickJSRR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppParallelRcppProgressreldistrlangrmarkdownrpartRSpectrarstanrstantoolsrstudioapirsvdRtsneS4ArraysS4VectorssassScaledMatrixscalesscaterscuttleSingleCellExperimentsitmosnowSparseArrayStanHeadersstatmodstringistringrSummarizedExperimentsyssystemfontstensorAtextshapingtibbletinytexUCSC.utilsutf8uwotvctrsviporviridisviridisLitewithrxfunXVectoryamlzlibbioc
