Function reference • scFlow

Import and Export
`read_celltype_mappings()`	Read Celltype Mappings
`read_sce()`	Read a SingleCellExperiment from a folder
`read_sparse_matrix()`	Read a feature-barcode matrix
`write_celltype_mappings()`	Write Celltype Mappings
`write_sce()`	Write a SingleCellExperiment to a folder
`write_sparse_matrix()`	Write a feature-barcode matrix
Pre-Processing and Annotation
`annotate_celltype_metrics()`	Annotate a SingleCellExperiment With Cell-type Metrics
`annotate_integrated_sce()`	Annotate integrated, reduced dimension, and clustered SingleCellExperiment object
`annotate_merged_sce()`	Annotate a post-merge SingleCellExperiment with plots
`annotate_sce()`	Annotate a SingleCellExperiment With Gene Names and QC Metrics
`annotate_sce_cells()`	Add basic cell-wise annotations for a SingleCellExperiment
`annotate_sce_genes()`	Add basic gene-wise annotations for a SingleCellExperiment
`filter_sce()`	Filter SingleCellExperiment according to QC metrics Quality control metrics previously calculated are used to subset the SingleCellExperiment for both cells and genes passing QC criteria previously specified in the `annotate_sce_genes` and `annotate_sce_cells` functions
`find_cells()`	Annotate a SingleCellExperiment with EmptyDrops predictions
`find_singlets()`	Find singlets in a SingleCellExperiment
`generate_sce()`	Generate a SingleCellExperiment object from a matrix and metadata
`map_ensembl_gene_id()`	Return mappings for Ensembl Gene IDs
`merge_sce()`	Merge Multiple SingleCellExperiment Objects
`read_metadata()`	Read the metadata for a sample from a samplesheet
`report_celltype_metrics()`	Generate A Report of Cell-Type Metrics for a SingleCellExperiment
`report_celltype_model()`	Generate a report for a celltype proportion analysis
`report_merged_sce()`	Generate plots and a QC report for a SingleCellExperiment
`report_qc_sce()`	Generate plots and a QC report for a SingleCellExperiment
Clustering and Dimensionality Reduction
`cluster_sce()`	Cluster SingleCellExperiment with monocle3::cluster_cells
`map_custom_celltypes()`	Map Custom Celltype Annotations from a DataFrame
`reduce_dims_sce()`	Calculate dimensionality reductions for a SingleCellExperiment object or merged SingleCellExperiment objects using tSNE, UMAP, UMAP3D
Differential Gene Expression
`perform_de()`	Perform Differential Gene Expression on a SingleCellExperiment
`pseudobulk_sce()`	Generate a Pseudo-bulk SingleCellExperiment from a SingleCellExperiment
`report_de()`	Generate a report for differential expression analysis
`volcano_plot()`	Plot volcano plot for differential expression analysis
Data Visualization
`plot_expr_by_numeric_var()`	Plot Gene Expression for Samples against Numerical Variable
`plot_reduced_dim()`	Plot Cells Reduced Dimensions With Feature Highlighting
`plot_reduced_dim_gene()`	Plot Cells Reduced Dimensions With Gene Expression
`plot_violin()`	Plot Gene Expression Violin Plots Stratified by Group
Impacted Pathway Analysis
`find_impacted_pathways()`	Functional enrichment analysis
`list_databases()`	Check available databases and their alias for scFlow
`pathway_analysis_enrichr()`	Functional enrichment analysis using enrichR
`pathway_analysis_webgestaltr()`	Functional enrichment analysis using WebgestaltR
`report_impacted_pathway()`	Generate a report for impacted pathway analysis
Data Integration
`integrate_sce()`	Integrate datasets within a SingleCellExperiment Object
`liger_preprocess()`	Preprocessing steps for Liger dimensionality reduction
`liger_reduce_dims()`	Dimensionality reduction using Liger factorization
`report_integrated_sce()`	Generate a report for dataset integration, dims reduction, and clustering
Celltype annotation
`find_marker_genes()`	Find specific markers for groups of cells
`map_celltypes_sce()`	Map cluster celltypes with EWCE
`model_celltype_freqs()`	Model Changes in Celltype Frequencies with Dirichlet Multinomial Regression

Reference

Import and Export

Pre-Processing and Annotation

Clustering and Dimensionality Reduction

Differential Gene Expression

Data Visualization

Impacted Pathway Analysis

Data Integration

Celltype annotation