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RaceID
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]
[Scholar Profile | Author Map]
All associated links for this package
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 21 Dec. 2024.
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
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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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