Package: RaceID 0.3.6

Dominic Grün

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]

RaceID_0.3.6.tar.gz
RaceID_0.3.6.tar.gz(r-4.5-noble)RaceID_0.3.6.tar.gz(r-4.4-noble)
RaceID_0.3.6.tgz(r-4.4-emscripten)RaceID_0.3.6.tgz(r-4.3-emscripten)
RaceID.pdf |RaceID.html
RaceID/json (API)

# Install 'RaceID' in R:
install.packages('RaceID', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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

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

4.52 score 110 scripts 471 downloads 25 mentions 102 exports 81 dependencies

Last updated 3 days agofrom:0a80b58a40. Checks:OK: 2. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-linux-x86_64OKOct 27 2024

Exports:barplotgenebaseLineVarbranchcellscalcAlphaGcalcVarcalcVarFitCCcorrectcellsfromtreecleanNNclustdiffgenesclustexpclustheatmapcompdistcompentropycompfrcompMeancompmedoidscompNoisecomppvaluecompscorecompTBNoisecomptsnecompumapcorrVarcreateKnnMatrixdiffexpnbdiffgenesdiffNoisyGenesdiffNoisyGenesTBextractCountsfilterdatafindoutliersfitBackVarfitGammaRtfitLogVarLogMeanfitNBtbfitNBtbClfractDotPlotgetExpDatagetfdatagetFilteredCountsgetNodegetprojgraphClusterimputeexpinspectKNNlineagegraphLtreemaxNoisyGenesmaxNoisyGenesTBnoiseBaseFitplotBplotbackgroundplotBackVarplotdiffgenesplotdiffgenesnbplotDiffNoiseplotdimsatplotdistanceratioplotexpmapplotExpNoiseplotfeatmapplotgraphplotjaccardplotlabelsmapplotlinkpvplotlinkscoreplotmapplotmarkergenesplotMVplotNoiseModelplotoutlierprobsplotPCplotPearsonResplotPPplotPTplotQQplotQuantMapplotRegNBplotsaturationplotsensitivityplotsilhouetteplotspantreeplotsymbolsmapplotTrProbsplotUMINoisepostfntbpriorfnprojbackprojcellsprojenrichmentpruneKnnpseudoTimequantKnnrfcorrectSCseqSeurat2SCseqtestPriortransitionProbsupdateSCvarRegressionviolinMarkerPlot

Dependencies:askpassclasscliclustercolorspacecoopcowplotcpp11DEoptimRdiptestdplyrfansifarverFateIDflexmixFNNfpcgenericsggplot2gluegtableharmonyhereicaigraphirlbaisobandjsonlitekernlablabelinglatticeleidenlifecyclelocfitmagrittrMASSMatrixmatrixStatsmclustmgcvmodeltoolsmunsellnlmennetopensslpermutepheatmappillarpkgconfigpngprabclusprincurvequadprogR6randomForestrappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppProgressRcppTOMLreticulateRhpcBLASctlrlangrobustbaserprojrootRSpectraRtsnerunnerscalessomsystibbletidyselectumaputf8vctrsveganviridisLitewithr

RaceID/StemID/VarID reference manual

Rendered fromRaceID.Rmdusingknitr::rmarkdownon Oct 27 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq DataRaceID-package RaceID
Gene Expression Barplotbarplotgene
Baseline gene expression variabilitybaseLineVar
Differential Gene Expression between Linksbranchcells
Function for calculating an aggregated dispersion parametercalcAlphaG
Function for calculating total variance from VarID fitcalcVar
Function for calculating the total variance fitcalcVarFit
Cell cycle markers for Mus Muscuuscc_genes
Dimensional Reduction by PCA or ICACCcorrect
Extract Cells on Differentiation Trajectorycellsfromtree
Function for pruning k-nearest neighborhoods based on neighborhood overlapcleanNN
Inference of differentially expressed genes in a clusterclustdiffgenes
Clustering of single-cell transcriptome dataclustexp
Plotting a Heatmap of the Distance Matrixclustheatmap
Computing a distance matrix for cell type inferencecompdist
Compute transcriptome entropy of each cellcompentropy
Computation of a two dimensional Fruchterman-Rheingold representationcompfr
Function for computing local gene expression averagescompMean
Computes Medoids from a Clustering Partitioncompmedoids
Function for computing local gene expression variabilitycompNoise
Computing P-values for Link Significancecomppvalue
Compute StemID2 scorecompscore
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 representationcomptsne
Computation of a two dimensional umap representationcompumap
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 matrixcreateKnnMatrix
Function for differential expression analysisdiffexpnb
Compute Expression Differences between Clustersdiffgenes
Function for extracting genes with elevated variability in a clusterdiffNoisyGenes
Function for extracting genes with differential biological variability in a clusterdiffNoisyGenesTB
Function for filtering count dataextractCounts
Data filteringfilterdata
Inference of outlier cells and final clusteringfindoutliers
Function for computing a background model of gene expression variabilityfitBackVar
Fitting a Gamma distribution to global cell-to-cell variabilityfitGammaRt
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 variabilityfitNBtb
Function for fitting a negative binomial noise model of technical and biological variabilityfitNBtbCl
Dotplot of gene expression across clusters or samplesfractDotPlot
Function for extracting a filtered expression matrix from a 'RaceID' 'SCseq' objectgetExpData
Extracting filtered expression datagetfdata
Function for filtering count datagetFilteredCounts
Extract all genes for a module in a FateID self-orgaizing mapgetNode
Extract Projections of all Cells from a Clustergetproj
Function for infering clustering of the pruned k nearest neighbour graphgraphCluster
Imputed expression matriximputeexp
Function for inspecting pruned k-nearest neighbourhoodsinspectKNN
Single-cell transcriptome data of intestinal epithelial cellsintestinalData
Single-cell transcriptome data of intestinal epithelial cellsintestinalDataSmall
Inference of a Lineage Graphlineagegraph
The Ltree ClassLtree Ltree-class
Function for extracting genes maximal variabilitymaxNoisyGenes
Function for extracting genes maximal variabilitymaxNoisyGenesTB
Function for computing a fit to the baseline of gene expression variabilitynoiseBaseFit
Boxplots for features across clustersplotB
Plot Background Modelplotbackground
Function for plottinhg the background model of gene expression variabilityplotBackVar
Barplot of differentially expressed genesplotdiffgenes
Function for plotting differentially expressed genesplotdiffgenesnb
Function for plotting differentially variable genesplotDiffNoise
Plotting the Saturation of Explained Varianceplotdimsat
Histogram of Cell-to-Cell Distances in Real versus Embedded Spaceplotdistanceratio
Highlighting gene expression in a dimensional reduction representationplotexpmap
Noise-expression scatter plotplotExpNoise
Highlighting feature values in a dimensional reduction representationplotfeatmap
StemID2 Lineage Graphplotgraph
Plot Jaccard Similaritiesplotjaccard
Plot labels in a dimensional reduction representationplotlabelsmap
Heatmap of Link P-valuesplotlinkpv
Heatmap of Link Scoresplotlinkscore
Plotting a dimensional reduction representationplotmap
Plotting a Heatmap of Marker Gene Expressionplotmarkergenes
Plot of Mean-Variance dependence and various fitsplotMV
Function for plotting the baseline model of gene expression variabilityplotNoiseModel
Plot Outlier Probabilitiesplotoutlierprobs
Function to plot the selected number of principal componentsplotPC
Function for plotting the variance of Pearson residualsplotPearsonRes
Plotting function for posterior checksplotPP
Plotting pseudo-time in dimensional reduction representationplotPT
Scatter plot of two noise-related quantaties of local pruned k-nearest neighbourhoodsplotQQ
Plotting noise-related quantaties of local pruned k-nearest neighbourhoodsplotQuantMap
Function for plotting negative binomial regressionplotRegNB
Plot Saturation of Within-Cluster Dispersionplotsaturation
Plot Sensitivityplotsensitivity
Plot Cluster Silhouetteplotsilhouette
Minimum Spanning Tree of RaceID3 clustersplotspantree
Plotting groups as different symbols in a dimensional reduction representationplotsymbolsmap
Function for plotting transition probabilities between clustersplotTrProbs
Plotting noise dependence on total UMI countplotUMINoise
Posterior probabilitypostfntb
Prior function for maximum a posterior inferencepriorfn
Compute Cell Projections for Randomized Background Distributionprojback
Compute transcriptome entropy of each cellprojcells
Enrichment of cells on inter-cluster linksprojenrichment
Function inferring a pruned knn matrixpruneKnn
Extract pseudo-time order of cells along a trajectorypseudoTime
Noise-related quantaties of local pruned k-nearest neighbourhoodsquantKnn
Simple function using Rcpprcpp_hello_world
Random Forests-based Reclassificationrfcorrect
The SCseq ClassSCseq SCseq-class
Converting a Seurat object to a RaceID/VarID objectSeurat2SCseq
Posterior check of the modeltestPrior
Function for the computation of transition probabilities between clusterstransitionProbs
Function for updating a RaceID SCseq object with VarID resultsupdateSC
Linear Regression of Sources of VariabilityvarRegression
Violin plot of marker gene expression or noiseviolinMarkerPlot