Man pages for MarioniLab/scran
Methods for Single-Cell RNA-Seq Data Analysis
| buildSNNGraph | Build a nearest-neighbor graph |
| clusterCells | Cluster cells in a SingleCellExperiment |
| combineBlocks | Combine blockwise statistics |
| combineMarkers | Combine pairwise DE results into a marker list |
| combinePValues | Combine p-values |
| combineVar | Combine variance decompositions |
| computeMinRank | Compute the minimum rank |
| computeSumFactors | Normalization by deconvolution |
| convertTo | Convert to other classes |
| correlateGenes | Per-gene correlation statistics |
| correlateNull | Build null correlations |
| correlatePairs | Test for significant correlations |
| 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 |
| 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 |
| fixedPCA | PCA with a fixed number of components |
| 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 |
| quickSubCluster | Quick and dirty subclustering |
| rhoToPValue | Spearman's rho to a p-value |
| sandbag | Cell cycle phase training |
| scaledColRanks | Compute scaled column ranks |
| scoreMarkers | Score marker genes |
| summaryMarkerStats | Summary marker statistics |
| testLinearModel | Hypothesis tests with linear models |
