.assignIndicesToWorkers | Developer utilities |
.bpNotSharedOrUp | Developer utilities |
.checkCountMatrix | Developer utilities |
.ranksafeQR | Developer utilities |
.splitColsByWorkers | Developer utilities |
.splitRowsByWorkers | Developer utilities |
.splitVectorByWorkers | Developer utilities |
.subset2index | Developer utilities |
.unpackLists | Developer utilities |
addPerCellQC | Add QC metrics to a SummarizedExperiment |
addPerFeatureQC | Add QC metrics to a SummarizedExperiment |
aggregateAcrossCells | Aggregate data across groups of cells |
aggregateAcrossCells-method | Aggregate data across groups of cells |
aggregateAcrossFeatures | Aggregate feature sets in a SummarizedExperiment |
calculateAverage | Calculate per-feature average counts |
calculateAverage-method | Calculate per-feature average counts |
calculateCPM | Calculate CPMs |
calculateCPM-method | Calculate CPMs |
calculateFPKM | Calculate FPKMs |
calculateTPM | Calculate TPMs |
calculateTPM-method | Calculate TPMs |
computeGeometricFactors | Compute geometric size factors |
computeLibraryFactors | Compute library size factors |
computeMedianFactors | Compute median-based size factors |
downsampleBatches | Downsample batches to equal coverage |
downsampleMatrix | Downsample a count matrix |
fitLinearModel | Fit a linear model |
geometricSizeFactors | Compute geometric size factors |
geometricSizeFactors-method | Compute geometric size factors |
isOutlier | Identify outlier values |
librarySizeFactors | Compute library size factors |
librarySizeFactors-method | Compute library size factors |
logNormCounts | Compute log-normalized expression values |
logNormCounts-method | Compute log-normalized expression values |
makePerCellDF | Create a per-cell data.frame |
makePerFeatureDF | Create a per-feature data.frame |
medianSizeFactors | Compute median-based size factors |
medianSizeFactors-method | Compute median-based size factors |
mockSCE | Mock up a SingleCellExperiment |
normalizeCounts | Compute normalized expression values |
normalizeCounts-method | Compute normalized expression values |
numDetectedAcrossCells | Number of detected expression values per group of cells |
numDetectedAcrossCells-method | Number of detected expression values per group of cells |
numDetectedAcrossFeatures | Number of detected expression values per group of features |
numDetectedAcrossFeatures-method | Number of detected expression values per group of features |
perCellQCMetrics | Per-cell quality control metrics |
perCellQCMetrics-method | Per-cell quality control metrics |
perFeatureQCMetrics | Per-feature quality control metrics |
perFeatureQCMetrics-method | Per-feature quality control metrics |
quickPerCellQC | Quick cell-level QC |
quickPerCellQC-method | Quick cell-level QC |
readSparseCounts | Read sparse count matrix from file |
scuttle-pkg | Single-cell utilities |
scuttle-utils | Developer utilities |
sumCountsAcrossCells | Sum expression across groups of cells |
sumCountsAcrossCells-method | Sum expression across groups of cells |
sumCountsAcrossFeatures | Sum counts across feature sets |
sumCountsAcrossFeatures-method | Sum counts across feature sets |
summarizeAssayByGroup | Summarize an assay by group |
summarizeAssayByGroup-method | Summarize an assay by group |
uniquifyFeatureNames | Make feature names unique |
whichNonZero | Find non-zero entries of a matrix |
whichNonZero-method | Find non-zero entries of a matrix |