# Methods for Single-Cell RNA-Seq Data Analysis

## Documentation for package ‘scran’ version 1.18.0

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

## Help Pages

B C D F G I M N O P Q S T misc

## -- B --

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

## -- C --

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

## -- D --

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

## -- F --

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

## -- G --

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

## -- I --

improvedCV2 | Defunct functions

## -- M --

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

## -- N --

neighborsToKNNGraph | Build a nearest-neighbor graph
neighborsToSNNGraph | Build a nearest-neighbor graph

## -- O --

orderClusterMST | Minimum spanning trees on cluster centroids
overlapExprs | Defunct functions

## -- P --

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

## -- Q --

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

## -- S --

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

## -- T --

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

## -- misc --

.logBH | BH correction on log-p-values