Methods for Single-Cell RNA-Seq Data Analysis


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Documentation for package ‘scran’ version 1.34.0

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.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 Combine p-values
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