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 |