Man pages for scran
Methods for Single-Cell RNA-Seq Data Analysis
| bootstrapCluster | Assess cluster stability by bootstrapping |
| buildSNNGraph | Build a nearest-neighbor graph |
| cleanSizeFactors | Clean size factors |
| clusterModularity | Compute the cluster-wise modularity |
| clusterPurity | Evaluate cluster purity |
| clusterSNNGraph | Wrappers for graph-based clustering |
| coassignProb | Compute coassignment probabilities |
| combineBlocks | Combine blockwise statistics |
| 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 |
| convertTo | Convert to other classes |
| correlateGenes | Per-gene correlation statistics |
| correlateNull | Build null correlations |
| correlatePairs | Test for significant correlations |
| createClusterMST | Minimum spanning trees on cluster centroids |
| cyclone | Cell cycle phase classification |
| decideTestsPerLabel | Decide tests for each label |
| defunct | Defunct functions |
| denoisePCA | Denoise expression with PCA |
| DM | Compute the distance-to-median statistic |
| doubletCells | Detect doublet cells |
| doubletCluster | Detect doublet clusters |
| doubletRecovery | Recover intra-sample doublets |
| findMarkers | 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 |
| gene_selection | Gene selection |
| getClusteredPCs | Use clusters to choose the number of PCs |
| getMarkerEffects | Get marker effect sizes |
| getTopHVGs | Identify HVGs |
| getTopMarkers | Get top markers |
| logBH | BH correction on log-p-values |
| modelGeneCV2 | Model the per-gene CV2 |
| modelGeneCV2WithSpikes | Model the per-gene CV2 with spike-ins |
| modelGeneVar | Model the per-gene variance |
| modelGeneVarByPoisson | Model the per-gene variance with Poisson noise |
| modelGeneVarWithSpikes | Model the per-gene variance with spike-ins |
| multiMarkerStats | Combine multiple sets of marker statistics |
| pairwiseBinom | Perform pairwise binomial tests |
| pairwiseTTests | Perform pairwise t-tests |
| pairwiseWilcox | Perform pairwise Wilcoxon rank sum tests |
| pseudoBulkDGE | Quickly perform pseudo-bulk DE analyses |
| pseudoBulkSpecific | Label-specific pseudo-bulk DE |
| quickCluster | Quick clustering of cells |
| quickPseudotime | Quick MST-based pseudotime |
| quickSubCluster | Quick and dirty subclustering |
| sandbag | Cell cycle phase training |
| scaledColRanks | Compute scaled column ranks |
| summaryMarkerStats | Summary marker statistics |
| testLinearModel | Hypothesis tests with linear models |
| testPseudotime | Test for differences along pseudotime |
