Package: RaceID 0.3.8

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 [aut, cre]

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RaceID/json (API)

# Install 'RaceID' in R:

install.packages('RaceID', repos = c('https://dgrun.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

cc_genes - Cell cycle markers for Mus Muscuus
intestinalData - Single-cell transcriptome data of intestinal epithelial cells
intestinalDataSmall - Single-cell transcriptome data of intestinal epithelial cells

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.74 score 110 scripts 621 downloads 25 mentions 102 exports 81 dependencies

Last updated 17 days agofrom:00d8405f48. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 06 2024
R-4.5-win-x86_64	OK	Nov 06 2024
R-4.5-linux-x86_64	OK	Nov 06 2024
R-4.4-win-x86_64	OK	Nov 06 2024
R-4.4-mac-x86_64	OK	Nov 06 2024
R-4.4-mac-aarch64	OK	Nov 06 2024
R-4.3-win-x86_64	OK	Nov 06 2024
R-4.3-mac-x86_64	OK	Nov 06 2024
R-4.3-mac-aarch64	OK	Nov 06 2024

Exports:barplotgene baseLineVar branchcells calcAlphaG calcVar calcVarFit CCcorrect cellsfromtree cleanNN clustdiffgenes clustexp clustheatmap compdist compentropy compfr compMean compmedoids compNoise comppvalue compscore compTBNoise comptsne compumap corrVar createKnnMatrix diffexpnb diffgenes diffNoisyGenes diffNoisyGenesTB extractCounts filterdata findoutliers fitBackVar fitGammaRt fitLogVarLogMean fitNBtb fitNBtbCl fractDotPlot getExpData getfdata getFilteredCounts getNode getproj graphCluster imputeexp inspectKNN lineagegraph Ltree maxNoisyGenes maxNoisyGenesTB noiseBaseFit plotB plotbackground plotBackVar plotdiffgenes plotdiffgenesnb plotDiffNoise plotdimsat plotdistanceratio plotexpmap plotExpNoise plotfeatmap plotgraph plotjaccard plotlabelsmap plotlinkpv plotlinkscore plotmap plotmarkergenes plotMV plotNoiseModel plotoutlierprobs plotPC plotPearsonRes plotPP plotPT plotQQ plotQuantMap plotRegNB plotsaturation plotsensitivity plotsilhouette plotspantree plotsymbolsmap plotTrProbs plotUMINoise postfntb priorfn projback projcells projenrichment pruneKnn pseudoTime quantKnn rfcorrect SCseq Seurat2SCseq testPrior transitionProbs updateSC varRegression violinMarkerPlot

Dependencies:askpass class cli cluster colorspace coop cowplot cpp11 DEoptimR diptest dplyr fansi farver FateID flexmix FNN fpc generics ggplot2 glue gtable harmony here ica igraph irlba isoband jsonlite kernlab labeling lattice leiden lifecycle locfit magrittr MASS Matrix matrixStats mclust mgcv modeltools munsell nlme nnet openssl permute pheatmap pillar pkgconfig png prabclus princurve quadprog R6 randomForest rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppProgress RcppTOML reticulate RhpcBLASctl rlang robustbase rprojroot RSpectra Rtsne runner scales som sys tibble tidyselect umap utf8 vctrs vegan viridisLite withr

RaceID/StemID/VarID reference manual

Dominic Grun

Rendered fromRaceID.Rmdusingknitr::rmarkdownon Nov 06 2024.

Last update: 2024-04-04
Started: 2018-07-27

Help page	Topics
Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data	RaceID-package RaceID
Gene Expression Barplot	barplotgene
Baseline gene expression variability	baseLineVar
Differential Gene Expression between Links	branchcells
Function for calculating an aggregated dispersion parameter	calcAlphaG
Function for calculating total variance from VarID fit	calcVar
Function for calculating the total variance fit	calcVarFit
Cell cycle markers for Mus Muscuus	cc_genes
Dimensional Reduction by PCA or ICA	CCcorrect
Extract Cells on Differentiation Trajectory	cellsfromtree
Function for pruning k-nearest neighborhoods based on neighborhood overlap	cleanNN
Inference of differentially expressed genes in a cluster	clustdiffgenes
Clustering of single-cell transcriptome data	clustexp
Plotting a Heatmap of the Distance Matrix	clustheatmap
Computing a distance matrix for cell type inference	compdist
Compute transcriptome entropy of each cell	compentropy
Computation of a two dimensional Fruchterman-Rheingold representation	compfr
Function for computing local gene expression averages	compMean
Computes Medoids from a Clustering Partition	compmedoids
Function for computing local gene expression variability	compNoise
Computing P-values for Link Significance	comppvalue
Compute StemID2 score	compscore
Function for fitting a negative binomial noise model of technical and biological variability across cells in pruned k-nearest neighbourhoods.	compTBNoise
Computation of a two dimensional t-SNE representation	comptsne
Computation of a two dimensional umap representation	compumap
Function for regressing out the mean-variance dependence. This function corrects for the systematic dependence of the variance on the mean by a local regression.	corrVar
Function to create a knn matrix	createKnnMatrix
Function for differential expression analysis	diffexpnb
Compute Expression Differences between Clusters	diffgenes
Function for extracting genes with elevated variability in a cluster	diffNoisyGenes
Function for extracting genes with differential biological variability in a cluster	diffNoisyGenesTB
Function for filtering count data	extractCounts
Data filtering	filterdata
Inference of outlier cells and final clustering	findoutliers
Function for computing a background model of gene expression variability	fitBackVar
Fitting a Gamma distribution to global cell-to-cell variability	fitGammaRt
Second order polynomial fit of mean-variance dependence This function corrects for the systematic dependence of the variance on the mean by a local regression.	fitLogVarLogMean
Function for fitting a negative binomial noise model of technical and biological variability	fitNBtb
Function for fitting a negative binomial noise model of technical and biological variability	fitNBtbCl
Dotplot of gene expression across clusters or samples	fractDotPlot
Function for extracting a filtered expression matrix from a 'RaceID' 'SCseq' object	getExpData
Extracting filtered expression data	getfdata
Function for filtering count data	getFilteredCounts
Extract all genes for a module in a FateID self-orgaizing map	getNode
Extract Projections of all Cells from a Cluster	getproj
Function for infering clustering of the pruned k nearest neighbour graph	graphCluster
Imputed expression matrix	imputeexp
Function for inspecting pruned k-nearest neighbourhoods	inspectKNN
Single-cell transcriptome data of intestinal epithelial cells	intestinalData
Single-cell transcriptome data of intestinal epithelial cells	intestinalDataSmall
Inference of a Lineage Graph	lineagegraph
The Ltree Class	Ltree Ltree-class
Function for extracting genes maximal variability	maxNoisyGenes
Function for extracting genes maximal variability	maxNoisyGenesTB
Function for computing a fit to the baseline of gene expression variability	noiseBaseFit
Boxplots for features across clusters	plotB
Plot Background Model	plotbackground
Function for plottinhg the background model of gene expression variability	plotBackVar
Barplot of differentially expressed genes	plotdiffgenes
Function for plotting differentially expressed genes	plotdiffgenesnb
Function for plotting differentially variable genes	plotDiffNoise
Plotting the Saturation of Explained Variance	plotdimsat
Histogram of Cell-to-Cell Distances in Real versus Embedded Space	plotdistanceratio
Highlighting gene expression in a dimensional reduction representation	plotexpmap
Noise-expression scatter plot	plotExpNoise
Highlighting feature values in a dimensional reduction representation	plotfeatmap
StemID2 Lineage Graph	plotgraph
Plot Jaccard Similarities	plotjaccard
Plot labels in a dimensional reduction representation	plotlabelsmap
Heatmap of Link P-values	plotlinkpv
Heatmap of Link Scores	plotlinkscore
Plotting a dimensional reduction representation	plotmap
Plotting a Heatmap of Marker Gene Expression	plotmarkergenes
Plot of Mean-Variance dependence and various fits	plotMV
Function for plotting the baseline model of gene expression variability	plotNoiseModel
Plot Outlier Probabilities	plotoutlierprobs
Function to plot the selected number of principal components	plotPC
Function for plotting the variance of Pearson residuals	plotPearsonRes
Plotting function for posterior checks	plotPP
Plotting pseudo-time in dimensional reduction representation	plotPT
Scatter plot of two noise-related quantaties of local pruned k-nearest neighbourhoods	plotQQ
Plotting noise-related quantaties of local pruned k-nearest neighbourhoods	plotQuantMap
Function for plotting negative binomial regression	plotRegNB
Plot Saturation of Within-Cluster Dispersion	plotsaturation
Plot Sensitivity	plotsensitivity
Plot Cluster Silhouette	plotsilhouette
Minimum Spanning Tree of RaceID3 clusters	plotspantree
Plotting groups as different symbols in a dimensional reduction representation	plotsymbolsmap
Function for plotting transition probabilities between clusters	plotTrProbs
Plotting noise dependence on total UMI count	plotUMINoise
Posterior probability	postfntb
Prior function for maximum a posterior inference	priorfn
Compute Cell Projections for Randomized Background Distribution	projback
Compute transcriptome entropy of each cell	projcells
Enrichment of cells on inter-cluster links	projenrichment
Function inferring a pruned knn matrix	pruneKnn
Extract pseudo-time order of cells along a trajectory	pseudoTime
Noise-related quantaties of local pruned k-nearest neighbourhoods	quantKnn
Simple function using Rcpp	rcpp_hello_world
Random Forests-based Reclassification	rfcorrect
The SCseq Class	SCseq SCseq-class
Converting a Seurat object to a RaceID/VarID object	Seurat2SCseq
Posterior check of the model	testPrior
Function for the computation of transition probabilities between clusters	transitionProbs
Function for updating a RaceID SCseq object with VarID results	updateSC
Linear Regression of Sources of Variability	varRegression
Violin plot of marker gene expression or noise	violinMarkerPlot

Package: RaceID 0.3.8

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

RaceID/StemID/VarID reference manual

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