# Methods for Single-Cell RNA-Seq Data Analysis

## Documentation for package ‘scran’ version 1.40.0

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

## Help Pages

.logBH | BH correction on log-p-values
bootstrapCluster | Defunct functions
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
clusterCells | Cluster cells in a SingleCellExperiment
clusterKNNGraph | Defunct functions
clusterModularity | Defunct functions
clusterPurity | Defunct functions
clusterSNNGraph | Defunct functions
coassignProb | Defunct functions
combineBlocks | Combine blockwise statistics
combineCV2 | Combine variance decompositions
combineMarkers | Combine pairwise DE results into a marker list
combinePValues | Defunct functions
combineVar | Combine variance decompositions
computeMinRank | Compute the minimum rank
computeSumFactors | Normalization by deconvolution
connectClusterMST | Defunct functions
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 | Defunct functions
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 | Defunct functions
doubletCluster | Defunct functions
doubletRecovery | Defunct functions
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
fixedPCA | PCA with a fixed number of components
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
orderClusterMST | Defunct functions
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 | Defunct functions
quickSubCluster | Quick and dirty subclustering
quickSubCluster-method | Quick and dirty subclustering
rhoToPValue | Spearman's rho to a p-value
sandbag | Cell cycle phase training
sandbag-method | Cell cycle phase training
scaledColRanks | Compute scaled column ranks
scoreMarkers | Score marker genes
scoreMarkers-method | Score marker genes
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 | Defunct functions
testVar | Defunct functions
trendVar | Defunct functions