libscran/scran_8hpp_source.html

#ifndef SCRAN_SCRAN_HPP

#define SCRAN_SCRAN_HPP


#include "utils/macros.hpp"


#include "aggregation/AggregateAcrossCells.hpp"

#include "aggregation/DownsampleByNeighbors.hpp"


#include "feature_set_enrichment/HypergeometricTail.hpp"

#include "feature_set_enrichment/ScoreFeatureSet.hpp"


#include "clustering/BuildSnnGraph.hpp"

#if __has_include("igraph.h")

#include "clustering/ClusterSnnGraph.hpp"

#endif


#include "differential_analysis/ScoreMarkers.hpp"


#include "feature_selection/ChooseHvgs.hpp"

#include "feature_selection/FitVarianceTrend.hpp"

#include "feature_selection/ModelGeneVariances.hpp"


#include "dimensionality_reduction/SimplePca.hpp"

#include "dimensionality_reduction/ResidualPca.hpp"

#include "dimensionality_reduction/MultiBatchPca.hpp"


#include "normalization/LogNormCounts.hpp"

#include "normalization/GroupedSizeFactors.hpp"

#include "normalization/MedianSizeFactors.hpp"

#include "normalization/CenterSizeFactors.hpp"

#include "normalization/ChoosePseudoCount.hpp"

#include "normalization/quick_grouped_size_factors.hpp"


#include "quality_control/FilterCells.hpp"

#include "quality_control/SuggestRnaQcFilters.hpp"

#include "quality_control/PerCellRnaQcMetrics.hpp"

#include "quality_control/SuggestAdtQcFilters.hpp"

#include "quality_control/PerCellAdtQcMetrics.hpp"

#include "quality_control/SuggestCrisprQcFilters.hpp"

#include "quality_control/PerCellCrisprQcMetrics.hpp"


#include "utils/average_vectors.hpp"

#include "utils/subset_vector.hpp"

#include "utils/vector_to_pointers.hpp"


namespace scran {}


#endif

AggregateAcrossCells.hpp
Aggregate expression values across cells.

BuildSnnGraph.hpp
Build a shared nearest-neighbor graph on the cells.

CenterSizeFactors.hpp
Center size factors prior to normalization.

ChooseHvgs.hpp
Choose highly variable genes for downstream analyses.

ChoosePseudoCount.hpp
Choose a suitable pseudo-count.

ClusterSnnGraph.hpp
Identify clusters of cells from a shared nearest-neighbor graph.

DownsampleByNeighbors.hpp
Downsample a dataset based on its neighbors.

FilterCells.hpp
Filter out low-quality cells from the count matrix.

FitVarianceTrend.hpp
Fit a mean-variance trend to log-count data.

GroupedSizeFactors.hpp
Compute size factors for groups of cells.

HypergeometricTail.hpp
Compute hypergeometric tail probabilities.

LogNormCounts.hpp
Compute log-normalized expression values.

MedianSizeFactors.hpp
Compute median-based size factors.

ModelGeneVariances.hpp
Model the per-gene variance from log-count data.

MultiBatchPca.hpp
Compute PCA after adjusting for differences between batch sizes.

PerCellAdtQcMetrics.hpp
Compute per-cell quality control metrics from an ADT count matrix.

PerCellCrisprQcMetrics.hpp
Compute per-cell quality control metrics from a CRISPR guide count matrix.

PerCellRnaQcMetrics.hpp
Compute typical per-cell quality control metrics from an RNA count matrix.

ResidualPca.hpp
Compute PCA after regressing out an uninteresting factor.

ScoreFeatureSet.hpp
Compute per-cell scores for a feature set.

ScoreMarkers.hpp
Compute marker scores for each gene in each group of cells.

SimplePca.hpp
Perform a simple PCA on a gene-by-cell matrix.

SuggestAdtQcFilters.hpp
Create filters to identify low-quality cells from ADT-derived QC metrics.

SuggestCrisprQcFilters.hpp
Create filters to identify low-quality cells from CRISPR-derived QC metrics.

SuggestRnaQcFilters.hpp
Create filters to identify low-quality cells from RNA-derived QC metrics.

average_vectors.hpp
Average parallel elements across vectors.

macros.hpp
Set common macros used through libscran.

scran
Functions for single-cell RNA-seq analyses.
Definition AggregateAcrossCells.hpp:18

quick_grouped_size_factors.hpp
Quickly compute grouped size factors.

subset_vector.hpp
Subset a vector easily.

vector_to_pointers.hpp
Create a vector of pointers from a vector of vectors.