Package index
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add_VDJ_metadata() - add_VDJ_metadata: Appends V(D)J alignments from CellRanger to an existing Seurat object
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calc_prelim_stats() - calc_prelim_stats: Calculates initial statistics for a Seurat object as required for downstream analysis
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calc_sc_gsea_score() - calc_sc_gsea_score: Calculates scores for pre-ranked GSEA
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cluster_metrics() - cluster_metrics: Calculates clustering metric scores
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convert_human_gene_list() - convert_human_gene_list
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convert_mtx_to_h5() - convert_mtx_to_h5: Converts the triple .mtx files from single cell experiments to a .h5 counts file
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fetch_celldex_ref() - fetch_celldex_ref: Helper function to import annotation references from celldex
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filter_cells() - filter_cells: A wrapper for multiple scRNA filtering methods
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filter_doublets() - filter_doublets: Identifies and removes doublets or multiplets in scRNA samples
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make_bubble_plot() - make_bubble_plot: Flexible dotplot
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make_volcano_plot() - make_volcano_plot: Optimized volcano plot for Seurat differential expression (FindMarkers) output
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preprocess_sample() - preprocess_sample: Performs an initial preprocess on a Seurat object
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run_AUCell() - run_AUCell: A wrapper script for running AUCell for per cell gene set enrichment analysis
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run_batch_correction() - run_batch_correction: Performs batch correction within Seurat v5 framework
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run_hypergeometric_test() - run_hypergeometric_test: Calculates the p-value of an overrepresentation test using the hypergeometric test
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run_singleR() - run_singleR: Runs SingleR directly on the Seurat object
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run_singleR_cluster() - run_singleR_cluster: Runs SingleR on average expression of clusters
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run_singleR_db() - run_singleR_db: Runs SingleR with the built-in databases from celldex
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seurat_clustering() - seurat_clustering: A quick end-to-end clustering of a Seurat object
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split_featurePlot() - split_featurePlot: Splits FeaturePlot by groups