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| buildSNNGraph | Build a SNN graph |
| buildSNNGraph-method | Build a SNN graph |
| 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 |
| 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 |
| denoisePCA | Denoise expression with PCA |
| denoisePCA-method | Denoise expression with PCA |
| DM | Compute the distance-to-median statistic |
| exploreData | Shiny app for explorative data analysis |
| 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 |
| isSpike<- | Set spike-in rows |
| isSpike<--method | Set spike-in rows |
| mnnCorrect | Mutual nearest neighbors correction |
| overlapExprs | Overlap expression profiles |
| overlapExprs-method | Overlap expression profiles |
| 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 |
| 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 |