# Bindings to C++ Libraries for Single-Cell Analysis

## Documentation for package ‘scrapper’ version 1.7.3

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

## Help Pages

A B C D E F G I L M N P Q R S T

scrapper-package | scrapper: Bindings to C++ Libraries for Single-Cell Analysis

## -- A --

adt_quality_control | Quality control for ADT count data
adt_quality_control_defaults | Default parameters for ADT quality control
aggregateAcrossCells | Aggregate expression across cells
aggregateAcrossCells.se | Aggregate expression across cells in a SummarizedExperiment
aggregateAcrossCellsDefaults | Default parameters for 'aggregateAcrossCells'
aggregateAcrossGenes | Aggregate expression across genes
aggregateAcrossGenes.se | Aggregate expression across gene sets in a SummarizedExperiment
aggregateAcrossGenesDefaults | Default parameters for 'aggregateAcrossGenes'
aggregateColData | Aggregate expression across cells in a SummarizedExperiment
analyze | Defunct functions
analyze.se | Analyze single-cell data from a SummarizedExperiment

## -- B --

buildSnnGraph | Build a shared nearest neighbor graph
buildSnnGraphDefaults | Default parameters for 'buildSnnGraph'

## -- C --

centerSizeFactors | Center size factors
centerSizeFactorsDefaults | Default parameters for 'centerSizeFactors'
centerSpikeInFactors | Center spike-in size factors
centerSpikeInFactorsDefaults | Default parameters for 'centerSpikeInFactors'
chooseHighlyVariableGenes | Choose highly variable genes
chooseHighlyVariableGenesDefaults | Default parameters for 'chooseHighlyVariableGenes'
choosePseudoCount | Choose a suitable pseudo-count
choosePseudoCountDefaults | Default parameters for 'choosePseudoCount'
chooseRnaHvgs.se | Choose highly variable genes from a SummarizedExperiment
chooseRnaHvgsWithSpikeIns.se | Choose highly variable genes based on spike-ins
clusterGraph | Graph-based clustering of cells
clusterGraph.se | Graph-based clustering of cells in a SingleCellExperiment
clusterGraphDefaults | Default parameters for 'clusterGraph'
clusterKmeans | K-means clustering
clusterKmeans.se | k-means clustering of cells in a SingleCellExperiment
clusterKmeansDefaults | Default parameters for 'clusterKmeans'
combineFactors | Combine multiple factors
computeAdtQcMetrics | Quality control for ADT count data
computeAdtQcMetricsDefaults | Default parameters for ADT quality control
computeBlockWeights | Compute block weights
computeBlockWeightsDefaults | Default parameters for 'computeBlockWeights'
computeClrm1Factors | Compute size factors for ADT counts
computeClrm1FactorsDefaults | Default parameters for 'computeClrm1Factors'
computeCrisprQcMetrics | Quality control for CRISPR count data
computeCrisprQcMetricsDefaults | Default parameters for CRISPR quality control
computeRnaQcMetrics | Quality control for RNA count data
computeRnaQcMetricsDefaults | Default parameters for RNA quality control
computeRnaQcMetricsWithAltExps | Quick quality control for RNA data in a SummarizedExperiment
convertAnalyzeResults | Defunct functions
correctMnn | Batch correction with mutual nearest neighbors
correctMnn.se | MNN correction on a SingleCellExperiment
correctMnnDefaults | Default parameters for 'correctMnn'
countGroupsByBlock | Count cells in groups and blocks
crispr_quality_control | Quality control for CRISPR count data
crispr_quality_control_defaults | Default parameters for CRISPR quality control

## -- D --

DelayedArray-method | Delayed log-normalization of a matrix
dim-method | Delayed log-normalization of a matrix
dimnames-method | Delayed log-normalization of a matrix

## -- E --

extract_array-method | Delayed log-normalization of a matrix
extract_sparse_array-method | Delayed log-normalization of a matrix

## -- F --

filterAdtQcMetrics | Quality control for ADT count data
filterCrisprQcMetrics | Quality control for CRISPR count data
filterRnaQcMetrics | Quality control for RNA count data
fitVarianceTrend | Fit a mean-variance trend
fitVarianceTrendDefaults | Default parameters for 'fitVarianceTrend'
formatComputeAdtQcMetricsResult | Quick quality control for ADT data in a SummarizedExperiment
formatComputeCrisprQcMetricsResult | Quick quality control for CRISPR data in a SummarizedExperiment
formatComputeRnaQcMetricsResult | Quick quality control for RNA data in a SummarizedExperiment
formatModelGeneVariancesResult | Choose highly variable genes from a SummarizedExperiment
formatScoreMarkersResult | Score marker genes in a SummarizedExperiment

## -- G --

getTestAdtData.se | Get datasets for testing
getTestCrisprData.se | Get datasets for testing
getTestData.se | Get datasets for testing
getTestRnaData.se | Get datasets for testing

## -- I --

initializeCpp-method | Delayed log-normalization of a matrix
is_sparse-method | Delayed log-normalization of a matrix

## -- L --

LogNormalizedMatrix | Delayed log-normalization of a matrix
LogNormalizedMatrix-class | Delayed log-normalization of a matrix
LogNormalizedMatrixSeed | Delayed log-normalization of a matrix
LogNormalizedMatrixSeed-class | Delayed log-normalization of a matrix

## -- M --

matrixClass-method | Delayed log-normalization of a matrix
modelGeneVariances | Model per-gene variances in expression
modelGeneVariancesDefaults | Default parameters for 'modelGeneVariances'

## -- N --

normalizeAdtCounts.se | Normalize ADT counts in a SummarizedExperiment
normalizeCounts | Normalize the count matrix
normalizeCountsDefaults | Default parameters for 'normalizeCounts'
normalizeCrisprCounts.se | Normalize CRISPR counts in a SummarizedExperiment
normalizeRnaCounts.se | Normalize RNA counts in a SummarizedExperiment
normalizeRnaCountsWithSpikeIns.se | Normalize RNA and spike-in counts

## -- P --

previewMarkers | Score marker genes in a SummarizedExperiment

## -- Q --

quickAdtQc.se | Quick quality control for ADT data in a SummarizedExperiment
quickCrisprQc.se | Quick quality control for CRISPR data in a SummarizedExperiment
quickRnaQc.se | Quick quality control for RNA data in a SummarizedExperiment

## -- R --

reportGroupMarkerStatistics | Report marker statistics for a single group
rna_quality_control | Quality control for RNA count data
rna_quality_control_defaults | Default parameters for RNA quality control
runAllNeighborSteps | Run all neighbor-related steps
runAllNeighborSteps.se | Run all nearest neighbor steps on a SummarizedExperiment
runPca | Principal components analysis
runPca.se | Principal components analysis of a Summarizedexperiment
runPcaDefaults | Default parameters for 'runPca'
runTsne | t-stochastic neighbor embedding
runTsne.se | t-SNE on a SummarizedExperiment
runTsneDefaults | Default parameters for 'runTsne'
runUmap | Uniform manifold approximation and projection
runUmap.se | UMAP on a SummarizedExperiment
runUmapDefaults | Default parameters for 'runUmap'

## -- S --

sanitizeSizeFactors | Sanitize size factors
sanitizeSizeFactorsDefaults | Default parameters for 'sanitizeSizeFactors'
scaleByNeighbors | Scale and combine multiple embeddings
scaleByNeighbors.se | Scale and combine multiple embeddings in a SingleCellExperiment
scaleByNeighborsDefaults | Default parameters for 'scaleByNeighbors'
scoreGeneSet | Score gene set activity for each cell
scoreGeneSet.se | Score a gene set in a SummarizedExperiment
scoreGeneSetDefaults | Default parameters for 'scoreGeneSet'
scoreMarkers | Score marker genes
scoreMarkers.se | Score marker genes in a SummarizedExperiment
scoreMarkersDefaults | Default parameters for 'scoreMarkers'
scrapper | scrapper: Bindings to C++ Libraries for Single-Cell Analysis
subsampleByNeighbors | Subsample cells based on their neighbors
subsampleByNeighborsDefaults | Default parameters for 'subsampleByNeighbors'
subsampleByPartition | Subsample by partition
subsampleByPartitionDefaults | Default parameters for 'subsampleByPartition'
suggestAdtQcThresholds | Quality control for ADT count data
suggestAdtQcThresholdsDefaults | Default parameters for ADT quality control
suggestCrisprQcThresholds | Quality control for CRISPR count data
suggestCrisprQcThresholdsDefaults | Default parameters for CRISPR quality control
suggestRnaQcThresholds | Quality control for RNA count data
suggestRnaQcThresholdsDefaults | Default parameters for RNA quality control
summarizeEffects | Summarize pairwise effect sizes for each group
summarizeEffectsDefaults | Default parameters for 'summarizeEffectsDefaults'

## -- T --

testEnrichment | Test for gene set enrichment
testEnrichmentDefaults | Default parameters for 'testEnrichment'
tsnePerplexityToNeighbors | t-stochastic neighbor embedding
type-method | Delayed log-normalization of a matrix