Bindings to C++ Libraries for Single-Cell Analysis

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Documentation for package ‘scrapper’ version 1.1.14

• 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
aggregateAcrossGenes	Aggregate expression across genes
analyze	Analyze single-cell data
buildSnnGraph	Build a shared nearest neighbor graph
centerSizeFactors	Center size factors
chooseHighlyVariableGenes	Choose highly variable genes
choosePseudoCount	Choose a suitable pseudo-count
clusterGraph	Graph-based clustering of cells
clusterKmeans	K-means clustering
combineFactors	Combine multiple factors
computeAdtQcMetrics	Quality control for ADT count data
computeClrm1Factors	Compute size factors for ADT counts
computeCrisprQcMetrics	Quality control for CRISPR count data
computeRnaQcMetrics	Quality control for RNA count data
convertAnalyzeResults	Convert analysis results into a SingleCellExperiment
correctMnn	Batch correction with mutual nearest neighbors
crispr_quality_control	Quality control for CRISPR count data
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
modelGeneVariances	Model per-gene variances in expression
normalizeCounts	Normalize the count matrix
reportGroupMarkerStatistics	Report marker statistics for a single group
rna_quality_control	Quality control for RNA count data
runAllNeighborSteps	Run all neighbor-related steps
runPca	Principal components analysis
runTsne	t-stochastic neighbor embedding
runUmap	Uniform manifold approxation and projection
sanitizeSizeFactors	Sanitize size factors
scaleByNeighbors	Scale and combine multiple embeddings
scoreGeneSet	Score gene set activity for each cell
scoreMarkers	Score marker genes
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