Methods for Single-Cell RNA-Seq Data Analysis


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Documentation for package ‘scran’ version 1.0.4

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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
normalize Compute normalized expression values
normalize-method Compute normalized expression values
quickCluster Quick clustering of cells
quickCluster-method Quick clustering of cells
sandbag Cell cycle phase training
sandbag-method Cell cycle phase training
spikes Construct the spike-in matrix
spikes-method Construct the spike-in matrix
testVar Test for significantly large variances
trendVar Get the biological variability
trendVar-method Get the biological variability