| 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 |
| 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 |
| 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 |
| simpleSumFactors | Quickly compute size factors via summation |
| simpleSumFactors-method | Quickly compute size factors via summation |
| 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 |