Package: nebula 1.5.3

nebula: Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data

A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.

Authors:Liang He [aut, cre], Raghav Sharma [ctb]

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Bug tracker:https://github.com/lhe17/nebula/issues

On CRAN:

4 exports 28 stars 2.47 score 173 dependencies 139 scripts 310 downloads

Last updated 7 months agofrom:e17fb830b6. Checks:OK: 1 NOTE: 8. Indexed: yes.

Exports:group_cellnbresidualnebulascToNeb

Dependencies:abindaskpassbase64encBHBiobaseBiocGenericsbitopsbslibcachemcaToolscliclustercodetoolscolorspacecommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDelayedArraydeldirdigestdoFuturedoRNGdotCall64dplyrdqrngevaluatefansifarverfastDummiesfastmapfitdistrplusFNNfontawesomeforeachfsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggrepelggridgesglobalsgluegoftestgplotsgridExtragtablegtoolsherehighrhtmltoolshtmlwidgetshttpuvhttricaigraphIRangesirlbaisobanditeratorsjquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleidenlifecyclelistenvlmtestmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmenloptropensslparallellypatchworkpbapplypillarpkgconfigplotlyplyrpngpolyclipprogressrpromisespurrrR6RANNrappdirsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppGSLRcppHNSWRcppParallelRcppProgressRcppTOMLRcppZigguratreshape2reticulateRfastrlangrmarkdownrngtoolsROCRrprojrootRSpectraRtsneS4ArraysS4VectorssassscalesscattermoresctransformSeuratSeuratObjectshinySingleCellExperimentsitmosourcetoolsspspamSparseArrayspatstat.dataspatstat.explorespatstat.geomspatstat.randomspatstat.sparsespatstat.univarspatstat.utilsstringistringrSummarizedExperimentsurvivalsystensortibbletidyrtidyselecttinytextrustUCSC.utilsutf8uwotvctrsviridisLitewithrxfunxtableXVectoryamlzlibbioczoo