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RaceID  

Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
View on CRAN: Click here


Download and install RaceID package within the R console
Install from CRAN:
install.packages("RaceID")

Install from Github:
library("remotes")
install_github("cran/RaceID")

Install by package version:
library("remotes")
install_version("RaceID", "0.3.9")



Attach the package and use:
library("RaceID")
Maintained by
Dominic Grün
[Scholar Profile | Author Map]
First Published: 2018-07-27
Latest Update: 2024-01-08
Description:
Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) ). '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) ).
How to cite:
Dominic Grün (2018). RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data. R package version 0.3.9, https://cran.r-project.org/web/packages/RaceID. Accessed 27 Mar. 2025.
Previous versions and publish date:
0.0.9 (2018-07-27 15:40), 0.1.0 (2018-07-29 15:40), 0.1.1 (2018-08-07 15:40), 0.1.2 (2018-11-13 13:10), 0.1.3 (2019-01-22 16:50), 0.1.4 (2019-09-20 14:40), 0.1.5 (2019-09-22 18:30), 0.1.6 (2019-11-21 11:40), 0.1.7 (2020-01-13 20:40), 0.1.8 (2020-02-26 13:00), 0.1.9 (2020-04-15 10:30), 0.2.0 (2020-05-20 16:30), 0.2.1 (2020-08-10 19:10), 0.2.2 (2020-10-08 00:40), 0.2.3 (2021-04-08 08:10), 0.2.4 (2022-07-19 21:10), 0.2.5 (2022-08-15 13:30), 0.2.6 (2022-08-19 15:00), 0.2.7 (2022-11-01 15:02), 0.2.8 (2022-11-16 08:20), 0.2.9 (2023-03-01 12:50), 0.3.0 (2023-03-13 13:10), 0.3.1 (2023-07-17 20:40), 0.3.2 (2023-08-10 16:20), 0.3.3 (2023-09-28 12:10), 0.3.4 (2024-01-08 21:00), 0.3.5 (2024-04-04 01:33), 0.3.6 (2024-10-26 20:10), 0.3.7 (2024-11-02 00:20), 0.3.8 (2024-11-05 18:10)
Other packages that cited RaceID R package
View RaceID citation profile
Other R packages that RaceID depends, imports, suggests or enhances
Complete documentation for RaceID
Functions, R codes and Examples using the RaceID R package
Some associated functions: CCcorrect . Ltree . RaceID-package . SCseq . barplotgene . baseLineVar . branchcells . calcAlphaG . calcVar . calcVarFit . cc_genes . cellsfromtree . cleanNN . clustdiffgenes . clustexp . clustheatmap . compMean . compNoise . compTBNoise . compdist . compentropy . compfr . compmedoids . comppvalue . compscore . comptsne . compumap . corrVar . createKnnMatrix . diffNoisyGenes . diffNoisyGenesTB . diffexpnb . diffgenes . extractCounts . filterdata . findoutliers . fitBackVar . fitGammaRt . fitLogVarLogMean . fitNBtb . fitNBtbCl . fractDotPlot . getExpData . getFilteredCounts . getNode . getfdata . getproj . graphCluster . imputeexp . inspectKNN . intestinalData . intestinalDataSmall . lineagegraph . maxNoisyGenes . maxNoisyGenesTB . noiseBaseFit . plotB . plotBackVar . plotDiffNoise . plotExpNoise . plotMV . plotNoiseModel . plotPC . plotPP . plotPT . plotPearsonRes . plotQQ . plotQuantMap . plotRegNB . plotTrProbs . plotUMINoise . plotbackground . plotdiffgenes . plotdiffgenesnb . plotdimsat . plotdistanceratio . plotexpmap . plotfeatmap . plotgraph . plotjaccard . plotlabelsmap . plotlinkpv . plotlinkscore . plotmap . plotmarkergenes . plotoutlierprobs . plotsaturation . plotsensitivity . plotsilhouette . plotspantree . plotsymbolsmap . postfntb . priorfn . projback . projcells . projenrichment . pruneKnn . pseudoTime . quantKnn . rcpp_hello_world . rfcorrect . testPrior . transitionProbs . updateSC . varRegression . violinMarkerPlot . 
Some associated R codes: RaceID.R . RaceID_utils.R . RcppExports.R . StemID.R . StemID_utils.R . VarID_functions.R . cc_genes.R . intestinalData.R . intestinalDataSmall.R .  Full RaceID package functions and examples
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