Bindings to C++ Libraries for Single-Cell Analysis

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Documentation for package ‘scrapper’ version 1.5.11

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

Help Pages

adt_quality_control	Quality control for ADT count data
aggregateAcrossCells	Aggregate expression across cells
aggregateAcrossCells.se	Aggregate expression across cells in a SummarizedExperiment
aggregateAcrossGenes	Aggregate expression across genes
aggregateAcrossGenes.se	Aggregate expression across gene sets in a SummarizedExperiment
aggregateColData	Aggregate expression across cells in a SummarizedExperiment
analyze	Analyze single-cell data
analyze.se	Analyze single-cell data from a SummarizedExperiment
buildSnnGraph	Build a shared nearest neighbor graph
centerSizeFactors	Center size factors
chooseHighlyVariableGenes	Choose highly variable genes
choosePseudoCount	Choose a suitable pseudo-count
chooseRnaHvgs.se	Choose highly variable genes from a SummarizedExperiment
clusterGraph	Graph-based clustering of cells
clusterGraph.se	Graph-based clustering of cells in a SingleCellExperiment
clusterKmeans	K-means clustering
clusterKmeans.se	k-means clustering of cells in a SingleCellExperiment
combineFactors	Combine multiple factors
computeAdtQcMetrics	Quality control for ADT count data
computeBlockWeights	Compute block weights
computeClrm1Factors	Compute size factors for ADT counts
computeCrisprQcMetrics	Quality control for CRISPR count data
computeRnaQcMetrics	Quality control for RNA count data
computeRnaQcMetricsWithAltExps	Quick quality control for RNA data in a SummarizedExperiment
convertAnalyzeResults	Convert analysis results into a SingleCellExperiment
correctMnn	Batch correction with mutual nearest neighbors
correctMnn.se	MNN correction on a SingleCellExperiment
countGroupsByBlock	Count cells in groups and blocks
crispr_quality_control	Quality control for CRISPR count data
DelayedArray-method	Delayed log-normalization of a matrix
dim-method	Delayed log-normalization of a matrix
dimnames-method	Delayed log-normalization of a matrix
extract_array-method	Delayed log-normalization of a matrix
extract_sparse_array-method	Delayed log-normalization of a matrix
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
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
getTestAdtData.se	Get datasets for testing
getTestCrisprData.se	Get datasets for testing
getTestData.se	Get datasets for testing
getTestRnaData.se	Get datasets for testing
initializeCpp-method	Delayed log-normalization of a matrix
is_sparse-method	Delayed log-normalization of a matrix
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
matrixClass-method	Delayed log-normalization of a matrix
modelGeneVariances	Model per-gene variances in expression
normalizeAdtCounts.se	Normalize ADT counts in a SummarizedExperiment
normalizeCounts	Normalize the count matrix
normalizeCrisprCounts.se	Normalize CRISPR counts in a SummarizedExperiment
normalizeRnaCounts.se	Normalize RNA counts in a SummarizedExperiment
previewMarkers	Score marker genes in a SummarizedExperiment
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
reportGroupMarkerStatistics	Report marker statistics for a single group
rna_quality_control	Quality control for RNA count data
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
runTsne	t-stochastic neighbor embedding
runTsne.se	t-SNE on a SummarizedExperiment
runUmap	Uniform manifold approxation and projection
runUmap.se	UMAP on a SummarizedExperiment
sanitizeSizeFactors	Sanitize size factors
scaleByNeighbors	Scale and combine multiple embeddings
scaleByNeighbors.se	Scale and combine multiple embeddings in a SingleCellExperiment
scoreGeneSet	Score gene set activity for each cell
scoreGeneSet.se	Score a gene set in a SummarizedExperiment
scoreMarkers	Score marker genes
scoreMarkers.se	Score marker genes in a SummarizedExperiment
subsampleByNeighbors	Subsample cells based on their neighbors
suggestAdtQcThresholds	Quality control for ADT count data
suggestCrisprQcThresholds	Quality control for CRISPR count data
suggestRnaQcThresholds	Quality control for RNA count data
summarizeEffects	Summarize pairwise effect sizes for each group
testEnrichment	Test for gene set enrichment
tsnePerplexityToNeighbors	t-stochastic neighbor embedding
type-method	Delayed log-normalization of a matrix