Methods for Single-Cell RNA-Seq Data Analysis


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Documentation for package ‘scran’ version 1.12.1

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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
cleanSizeFactors Sanitize size factors
clusterModularity Compute the cluster-wise modularity
combineMarkers Combine DE results to a marker set
combinePValues Combine p-values
combineVar Combine variance decompositions
computeSpikeFactors Normalization with spike-in counts
computeSpikeFactors-method Normalization with spike-in counts
computeSumFactors Normalization by deconvolution
computeSumFactors-method Normalization by deconvolution
convertTo Convert to other classes
convertTo-method Convert to other classes
correlateGenes Per-gene correlation statistics
correlateNull Test for significant correlations
correlatePairs Test for significant correlations
correlatePairs-method Test for significant correlations
cosineNorm Cosine normalize
cyclone Cell cycle phase classification
cyclone-method Cell cycle phase classification
decomposeVar Decompose the gene-level variance
decomposeVar-method Decompose the gene-level variance
denoisePCA Denoise expression with PCA
denoisePCA-method 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
fastMNN Fast mutual nearest neighbors correction
findMarkers Find marker genes
findMarkers-method Find marker genes
improvedCV2 Stably model the technical coefficient of variation
improvedCV2-method Stably model the technical coefficient of variation
makeTechTrend Make a technical trend
mnnCorrect Mutual nearest neighbors correction
multiBatchNorm Per-batch scaling normalization
multiBatchPCA Multi-batch PCA
multiBlockNorm Per-block scaling normalization
multiBlockVar Per-block variance statistics
overlapExprs Overlap expression profiles
overlapExprs-method Overlap expression profiles
pairwiseTTests Perform pairwise t-tests
pairwiseWilcox Perform pairwise Wilcoxon rank sum tests
parallelPCA Parallel analysis for PCA
parallelPCA-method Parallel analysis for PCA
quickCluster Quick clustering of cells
quickCluster-method Quick clustering of cells
sandbag Cell cycle phase training
sandbag-method Cell cycle phase training
scaledColRanks Compute scaled column ranks
scran-gene-selection Gene selection
technicalCV2 Model the technical coefficient of variation
technicalCV2-method Model the technical coefficient of variation
testVar Test for significantly large variances
trendVar Fit a variance trend
trendVar-method Fit a variance trend