Man pages for scran
Methods for Single-Cell RNA-Seq Data Analysis

bootstrapClusterAssess cluster stability by bootstrapping
buildSNNGraphBuild a nearest-neighbor graph
cleanSizeFactorsClean size factors
clusterModularityCompute the cluster-wise modularity
clusterPurityEvaluate cluster purity
clusterSNNGraphWrappers for graph-based clustering
coassignProbCompute coassignment probabilities
combineBlocksCombine blockwise statistics
combineMarkersCombine pairwise DE results into a marker list
combinePValuesCombine p-values
combineVarCombine variance decompositions
computeSpikeFactorsNormalization with spike-in counts
computeSumFactorsNormalization by deconvolution
convertToConvert to other classes
correlateGenesPer-gene correlation statistics
correlateNullBuild null correlations
correlatePairsTest for significant correlations
createClusterMSTMinimum spanning trees on cluster centroids
cycloneCell cycle phase classification
decideTestsPerLabelDecide tests for each label
defunctDefunct functions
denoisePCADenoise expression with PCA
DMCompute the distance-to-median statistic
doubletCellsDetect doublet cells
doubletClusterDetect doublet clusters
doubletRecoveryRecover intra-sample doublets
findMarkersFind marker genes
fitTrendCV2Fit a trend to the CV2
fitTrendPoissonGenerate a trend for Poisson noise
fitTrendVarFit a trend to the variances of log-counts
gene_selectionGene selection
getClusteredPCsUse clusters to choose the number of PCs
getMarkerEffectsGet marker effect sizes
getTopHVGsIdentify HVGs
getTopMarkersGet top markers
logBHBH correction on log-p-values
modelGeneCV2Model the per-gene CV2
modelGeneCV2WithSpikesModel the per-gene CV2 with spike-ins
modelGeneVarModel the per-gene variance
modelGeneVarByPoissonModel the per-gene variance with Poisson noise
modelGeneVarWithSpikesModel the per-gene variance with spike-ins
multiMarkerStatsCombine multiple sets of marker statistics
pairwiseBinomPerform pairwise binomial tests
pairwiseTTestsPerform pairwise t-tests
pairwiseWilcoxPerform pairwise Wilcoxon rank sum tests
pseudoBulkDGEQuickly perform pseudo-bulk DE analyses
pseudoBulkSpecificLabel-specific pseudo-bulk DE
quickClusterQuick clustering of cells
quickPseudotimeQuick MST-based pseudotime
quickSubClusterQuick and dirty subclustering
sandbagCell cycle phase training
scaledColRanksCompute scaled column ranks
summaryMarkerStatsSummary marker statistics
testLinearModelHypothesis tests with linear models
testPseudotimeTest for differences along pseudotime
scran documentation built on April 17, 2021, 6:09 p.m.