# Methods for Single-Cell RNA-Seq Data Analysis

## Documentation for package ‘scran’ version 1.10.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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