Package: RaceID 0.3.5

RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <doi:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <doi:10.1186/s13059-023-02974-1>).

Authors:Dominic Grün <[email protected]>

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RaceID/json (API)

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102 exports 3.60 score 81 dependencies 25 mentions 101 scripts 506 downloads

Last updated 6 months agofrom:5f0e825e25. Checks:OK: 9. Indexed: yes.

Exports:barplotgenebaseLineVarbranchcellscalcAlphaGcalcVarcalcVarFitCCcorrectcellsfromtreecleanNNclustdiffgenesclustexpclustheatmapcompdistcompentropycompfrcompMeancompmedoidscompNoisecomppvaluecompscorecompTBNoisecomptsnecompumapcorrVarcreateKnnMatrixdiffexpnbdiffgenesdiffNoisyGenesdiffNoisyGenesTBextractCountsfilterdatafindoutliersfitBackVarfitGammaRtfitLogVarLogMeanfitNBtbfitNBtbClfractDotPlotgetExpDatagetfdatagetFilteredCountsgetNodegetprojgraphClusterimputeexpinspectKNNlineagegraphLtreemaxNoisyGenesmaxNoisyGenesTBnoiseBaseFitplotBplotbackgroundplotBackVarplotdiffgenesplotdiffgenesnbplotDiffNoiseplotdimsatplotdistanceratioplotexpmapplotExpNoiseplotfeatmapplotgraphplotjaccardplotlabelsmapplotlinkpvplotlinkscoreplotmapplotmarkergenesplotMVplotNoiseModelplotoutlierprobsplotPCplotPearsonResplotPPplotPTplotQQplotQuantMapplotRegNBplotsaturationplotsensitivityplotsilhouetteplotspantreeplotsymbolsmapplotTrProbsplotUMINoisepostfntbpriorfnprojbackprojcellsprojenrichmentpruneKnnpseudoTimequantKnnrfcorrectSCseqSeurat2SCseqtestPriortransitionProbsupdateSCvarRegressionviolinMarkerPlot

Dependencies:askpassclasscliclustercolorspacecoopcowplotcpp11DEoptimRdiptestdplyrfansifarverFateIDflexmixFNNfpcgenericsggplot2gluegtableharmonyhereicaigraphirlbaisobandjsonlitekernlablabelinglatticeleidenlifecyclelocfitmagrittrMASSMatrixmatrixStatsmclustmgcvmodeltoolsmunsellnlmennetopensslpermutepheatmappillarpkgconfigpngprabclusprincurvequadprogR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRcppTOMLreticulateRhpcBLASctlrlangrobustbaserprojrootRSpectraRtsnerunnerscalessomsystibbletidyselectumaputf8vctrsveganviridisLitewithr