B C D F G I M N O P Q S T misc
bootstrapCluster | Assess cluster stability by bootstrapping |
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 |
calculateSumFactors | Normalization by deconvolution |
calculateSumFactors-method | Normalization by deconvolution |
cleanSizeFactors | Clean size factors |
clusterKNNGraph | Wrappers for graph-based clustering |
clusterKNNGraph-method | Wrappers for graph-based clustering |
clusterModularity | Compute the cluster-wise modularity |
clusterPurity | Evaluate cluster purity |
clusterPurity-method | Evaluate cluster purity |
clusterSNNGraph | Wrappers for graph-based clustering |
clusterSNNGraph-method | Wrappers for graph-based clustering |
coassignProb | Compute coassignment probabilities |
combineBlocks | Combine blockwise statistics |
combineCV2 | Combine variance decompositions |
combineMarkers | Combine pairwise DE results into a marker list |
combinePValues | Combine p-values |
combineVar | Combine variance decompositions |
computeSpikeFactors | Normalization with spike-in counts |
computeSumFactors | Normalization by deconvolution |
connectClusterMST | Minimum spanning trees on cluster centroids |
convertTo | Convert to other classes |
correlateGenes | Per-gene correlation statistics |
correlateNull | Build null correlations |
correlatePairs | Test for significant correlations |
correlatePairs-method | Test for significant correlations |
createClusterMST | Minimum spanning trees on cluster centroids |
cyclone | Cell cycle phase classification |
cyclone-method | Cell cycle phase classification |
decideTestsPerLabel | Decide tests for each label |
decomposeVar | Defunct functions |
defunct | Defunct functions |
denoisePCA | Denoise expression with PCA |
denoisePCANumber | 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 |
doubletRecovery | Recover intra-sample doublets |
doubletRecovery-method | Recover intra-sample doublets |
findMarkers | Find marker genes |
findMarkers-method | Find marker genes |
fitTrendCV2 | Fit a trend to the CV2 |
fitTrendPoisson | Generate a trend for Poisson noise |
fitTrendVar | Fit a trend to the variances of log-counts |
getClusteredPCs | Use clusters to choose the number of PCs |
getDenoisedPCs | Denoise expression with PCA |
getDenoisedPCs-method | Denoise expression with PCA |
getMarkerEffects | Get marker effect sizes |
getTopHVGs | Identify HVGs |
getTopMarkers | Get top markers |
improvedCV2 | Defunct functions |
makeTechTrend | Defunct functions |
modelGeneCV2 | Model the per-gene CV2 |
modelGeneCV2-method | Model the per-gene CV2 |
modelGeneCV2WithSpikes | Model the per-gene CV2 with spike-ins |
modelGeneCV2WithSpikes-method | Model the per-gene CV2 with spike-ins |
modelGeneVar | Model the per-gene variance |
modelGeneVar-method | Model the per-gene variance |
modelGeneVarByPoisson | Model the per-gene variance with Poisson noise |
modelGeneVarByPoisson-method | Model the per-gene variance with Poisson noise |
modelGeneVarWithSpikes | Model the per-gene variance with spike-ins |
modelGeneVarWithSpikes-method | Model the per-gene variance with spike-ins |
multiBlockNorm | Defunct functions |
multiBlockVar | Defunct functions |
multiMarkerStats | Combine multiple sets of marker statistics |
neighborsToKNNGraph | Build a nearest-neighbor graph |
neighborsToSNNGraph | Build a nearest-neighbor graph |
orderClusterMST | Minimum spanning trees on cluster centroids |
overlapExprs | Defunct functions |
pairwiseBinom | Perform pairwise binomial tests |
pairwiseBinom-method | Perform pairwise binomial tests |
pairwiseTTests | Perform pairwise t-tests |
pairwiseTTests-method | Perform pairwise t-tests |
pairwiseWilcox | Perform pairwise Wilcoxon rank sum tests |
pairwiseWilcox-method | Perform pairwise Wilcoxon rank sum tests |
parallelPCA | Defunct functions |
pseudoBulkDGE | Quickly perform pseudo-bulk DE analyses |
pseudoBulkDGE-method | Quickly perform pseudo-bulk DE analyses |
pseudoBulkSpecific | Label-specific pseudo-bulk DE |
pseudoBulkSpecific-method | Label-specific pseudo-bulk DE |
quickCluster | Quick clustering of cells |
quickCluster-method | Quick clustering of cells |
quickPseudotime | Quick MST-based pseudotime |
quickSubCluster | Quick and dirty subclustering |
quickSubCluster-method | Quick and dirty subclustering |
sandbag | Cell cycle phase training |
sandbag-method | Cell cycle phase training |
scaledColRanks | Compute scaled column ranks |
scran-gene-selection | Gene selection |
summarizeTestsPerLabel | Decide tests for each label |
summaryMarkerStats | Summary marker statistics |
summaryMarkerStats-method | Summary marker statistics |
technicalCV2 | Defunct functions |
testLinearModel | Hypothesis tests with linear models |
testLinearModel-method | Hypothesis tests with linear models |
testPseudotime | Test for differences along pseudotime |
testPseudotime-method | Test for differences along pseudotime |
testVar | Defunct functions |
trendVar | Defunct functions |
.logBH | BH correction on log-p-values |