Methods for Single-Cell RNA-Seq Data Analysis


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Documentation for package ‘scran’ version 1.18.5

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B C D F G I M N O P Q S T misc

-- B --

bootstrapCluster Assess cluster stability by bootstrapping
buildKNNGraph Build a nearest-neighbor graph
buildKNNGraph-method Build a nearest-neighbor graph
buildSNNGraph Build a nearest-neighbor graph
buildSNNGraph-method Build a nearest-neighbor graph

-- C --

calculateSumFactors Normalization by deconvolution
calculateSumFactors-method Normalization by deconvolution
cleanSizeFactors Clean size factors
clusterKNNGraph Wrappers for graph-based clustering
clusterKNNGraph-method Wrappers for graph-based clustering
clusterModularity Compute the cluster-wise modularity
clusterPurity Evaluate cluster purity
clusterPurity-method Evaluate cluster purity
clusterSNNGraph Wrappers for graph-based clustering
clusterSNNGraph-method Wrappers for graph-based clustering
coassignProb Compute coassignment probabilities
combineBlocks Combine blockwise statistics
combineCV2 Combine variance decompositions
combineMarkers Combine pairwise DE results into a marker list
combinePValues Combine p-values
combineVar Combine variance decompositions
computeSpikeFactors Normalization with spike-in counts
computeSumFactors Normalization by deconvolution
connectClusterMST Minimum spanning trees on cluster centroids
convertTo Convert to other classes
correlateGenes Per-gene correlation statistics
correlateNull Build null correlations
correlatePairs Test for significant correlations
correlatePairs-method Test for significant correlations
createClusterMST Minimum spanning trees on cluster centroids
cyclone Cell cycle phase classification
cyclone-method Cell cycle phase classification

-- D --

decideTestsPerLabel Decide tests for each label
decomposeVar Defunct functions
defunct Defunct functions
denoisePCA Denoise expression with PCA
denoisePCANumber Denoise expression with PCA
DM Compute the distance-to-median statistic
doubletCells Detect doublet cells
doubletCells-method Detect doublet cells
doubletCluster Detect doublet clusters
doubletCluster-method Detect doublet clusters
doubletRecovery Recover intra-sample doublets
doubletRecovery-method Recover intra-sample doublets

-- F --

findMarkers Find marker genes
findMarkers-method Find marker genes
fitTrendCV2 Fit a trend to the CV2
fitTrendPoisson Generate a trend for Poisson noise
fitTrendVar Fit a trend to the variances of log-counts

-- G --

getClusteredPCs Use clusters to choose the number of PCs
getDenoisedPCs Denoise expression with PCA
getDenoisedPCs-method Denoise expression with PCA
getMarkerEffects Get marker effect sizes
getTopHVGs Identify HVGs
getTopMarkers Get top markers

-- I --

improvedCV2 Defunct functions

-- M --

makeTechTrend Defunct functions
modelGeneCV2 Model the per-gene CV2
modelGeneCV2-method Model the per-gene CV2
modelGeneCV2WithSpikes Model the per-gene CV2 with spike-ins
modelGeneCV2WithSpikes-method Model the per-gene CV2 with spike-ins
modelGeneVar Model the per-gene variance
modelGeneVar-method Model the per-gene variance
modelGeneVarByPoisson Model the per-gene variance with Poisson noise
modelGeneVarByPoisson-method Model the per-gene variance with Poisson noise
modelGeneVarWithSpikes Model the per-gene variance with spike-ins
modelGeneVarWithSpikes-method Model the per-gene variance with spike-ins
multiBlockNorm Defunct functions
multiBlockVar Defunct functions
multiMarkerStats Combine multiple sets of marker statistics

-- N --

neighborsToKNNGraph Build a nearest-neighbor graph
neighborsToSNNGraph Build a nearest-neighbor graph

-- O --

orderClusterMST Minimum spanning trees on cluster centroids
overlapExprs Defunct functions

-- P --

pairwiseBinom Perform pairwise binomial tests
pairwiseBinom-method Perform pairwise binomial tests
pairwiseTTests Perform pairwise t-tests
pairwiseTTests-method Perform pairwise t-tests
pairwiseWilcox Perform pairwise Wilcoxon rank sum tests
pairwiseWilcox-method Perform pairwise Wilcoxon rank sum tests
parallelPCA Defunct functions
pseudoBulkDGE Quickly perform pseudo-bulk DE analyses
pseudoBulkDGE-method Quickly perform pseudo-bulk DE analyses
pseudoBulkSpecific Label-specific pseudo-bulk DE
pseudoBulkSpecific-method Label-specific pseudo-bulk DE

-- Q --

quickCluster Quick clustering of cells
quickCluster-method Quick clustering of cells
quickPseudotime Quick MST-based pseudotime
quickSubCluster Quick and dirty subclustering
quickSubCluster-method Quick and dirty subclustering

-- S --

sandbag Cell cycle phase training
sandbag-method Cell cycle phase training
scaledColRanks Compute scaled column ranks
scran-gene-selection Gene selection
summarizeTestsPerLabel Decide tests for each label
summaryMarkerStats Summary marker statistics
summaryMarkerStats-method Summary marker statistics

-- T --

technicalCV2 Defunct functions
testLinearModel Hypothesis tests with linear models
testLinearModel-method Hypothesis tests with linear models
testPseudotime Test for differences along pseudotime
testPseudotime-method Test for differences along pseudotime
testVar Defunct functions
trendVar Defunct functions

-- misc --

.logBH BH correction on log-p-values