Methods for Single-Cell RNA-Seq Data Analysis


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Documentation for package ‘scran’ version 1.2.2

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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
correlateNull Test for significant correlations
correlatePairs Test for significant correlations
correlatePairs-method Test for significant correlations
cyclone Cell cycle phase classification
cyclone-method Cell cycle phase classification
decomposeVar Decompose the gene-level variance
decomposeVar-method Decompose the gene-level variance
DM Compute the distance-to-median statistic
isSpike Construct the spike-in matrix
isSpike-method Construct the spike-in matrix
isSpike<- Construct the spike-in matrix
isSpike<--method Construct the spike-in matrix
quickCluster Quick clustering of cells
quickCluster-method Quick clustering of cells
sandbag Cell cycle phase training
sandbag-method Cell cycle phase training
selectorPlot Construct a selector plot via Shiny
spikes Construct the spike-in matrix
spikes-method Construct the spike-in matrix
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