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

## Documentation for package ‘scrapper’ version 1.2.0

- 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