Function reference • seuratTools

All functions
`Monocle2_diffex()`	Monocle2 differential expression
`SetDefaultAssay()`	Reset default assay
`add_census_slot()`	add census assay to a seurat object
`add_percent_mito()`	Annotate percent mitochondrial reads per cell
`add_read_count_col()`	Annotate Low Read Count Category
`allTranscripts()`	Plot All Transcripts Server
`allTranscriptsui()`	Plot All Transcripts UI Module
`annotate_cell_cycle()`	Annotate Cell Cycle
`annotate_excluded()`	Annotate Exclusion Criteria
`append_to_project_db()`	Update a database of seuratTools projects
`arrange_ptime_heatmaps()`	Arrange processed monocle CDS objects containing heatmaps
`assign_clusters_to_cds()`	Assign Clusters to CDS
`build_bigwig_db()`	Create a database of bigwigfiles
`by_row_corr_between_pt_heatmaps()`	calculate row-wise correlation between two dataframes
`calc_cor_across_heatmaps()`	calculate correlation between heatmap matrices in processed cds_gene_list
`calc_pseudotime_heatmap()`	calculate pseudotime heatmaps
`ccScore()`	Cell Cycle Score
`ccScoreui()`	Cell Cycle Score UI
`cells_selected()`	Title
`celltype_markers`	Retinal Cell Type Marker Genes
`changeEmbedParams()`	Change Embedding Parameters
`changeEmbedParamsui()`	Change Embedding Parameters UI
`clustering_workflow()`	Clustering Workflow
`combine_cols()`	Reformat Seurat Object Metadata
`combine_looms()`	Combine Loom Files
`convert_human_seu_to_mouse()`	Convert Seurat Objects from Human to Mouse
`convert_monoclev2_to_seuv3()`	Convert a Seurat V3 object to a Monocle v2 object
`convert_mouse_seu_to_human()`	Convert Seurat Objects from Mouse to Human
`convert_seu_list_to_multimodal()`	convert seurat list to multimodal object
`convert_seu_to_cds()`	Convert a Seurat Object to a Monocle Cell Data Set
`convert_seurat_to_sce()`	convert seurat object to cds
`convert_seuv3_to_monoclev2()`	Convert a Seurat V3 object to a Monocle v2 object
`convert_symbols_by_species()`	Convert gene symbols between mouse and human
`convert_v3_to_v5()`	Convert seurat object to seurat V5 format
`create_proj_matrix()`	Create a Table of single Cell Projects
`create_project_db()`	Create a database of seuratTools projects
`cross_check_heatmaps()`	Title
`cross_species_integrate()`	Integrate Seurat Objects from Mouse to Human
`default_helper()`	Default Shiny Helper
`diffex()`	Differential Expression
`diffexui()`	Differential Expression UI
`dockerSeuratApp()`	Create a seurat app on a shinyproxy docker instance
`.send_enrichr_query()`	Gene enrichment using Enrichr.
`dropdownButton()`	Custom Dropdown Button
`enframe_markers()`	Enframe seurat markers
`filter_low_rc_cells()`	Filter our Cells from Seurat below read count threshold
`filter_merged_seu()`	Filter a Single Seurat Object
`filter_merged_seus()`	Filter a List of Seurat Objects
`filter_rows_to_top()`	Filter Rows to Top
`findMarkers()`	Find Markers
`findMarkersui()`	Find Markers UI
`find_all_markers()`	Find All Markers
`flip_pseudotime()`	Flip Pseudotime
`format_new_metadata()`	Add Seurat Object Metadata
`format_pathway_table()`	Title
`gene_test_plot()`	Plot Gene expression over pseudotime on reference and query trajectories from cellAlign
`genes_to_transcripts()`	Gene Symbols to Ensembl Transcript Ids
`getEnrichedPathways()`	Get enriched pathways based on marker genes from EnrichR.
`get_meta()`	Get Metadata for a project
`get_transcripts_from_seu()`	Get Transcripts in Seurat Object
`global_cellalign()`	Global Alignment of two trajectories with cellAlign
`harmony_integrate()`	Integrate small datasets with harmony
`human_to_mouse_homologs`	Gene Homologs Between Human and Mouse
`integrateProj()`	Integrate Projects Server Function
`integrateProjui()`	Integrate Project UI
`integration_workflow()`	Integration Workflow
`label_transfer()`	Transfer Labels Between Seurat Objects
`learn_graph_by_resolution()`	Learn Monocle Graph by Resolution
`list_plot_types()`	Collate list of variables to be plotted
`load_bigwigs()`	Load Bigwigs
`load_counts_by_tximport()`	Run tximport on a set of cells
`load_meta()`	Load Sample Metadata for a given project
`load_seurat_from_proj()`	Load Seurat Files from a single project path
`load_seurat_path()`	Read in Gene and Transcript Seurat Objects
`local_cellalign()`	Align two trajectories via cellalign
`make_bigwig_db()`	Make Bigwig Database
`make_seuratTools_clean_names()`	Clean Vector of seuratTools Names
`mem_str()`	Profile the memory of an s4object
`merge_loom()`	scvelo_assay
`merge_small_seus()`	Merge Small Seurat Objects
`metadata_from_batch()`	Retrieve Metadata from Batch
`minimalSeuratApp()`	Create a minimal seurat app
`monocle()`	Monocle Server Module
`monocle_module_heatmap()`	Title
`monocleui()`	Monocle UI Module
`pad_sample_files()`	pad sample numbers to prep for armor
`pathwayEnrichment()`	pathway enrichment
`pathwayEnrichmentui()`	Title
`plotClustree()`	plot clustree server
`plotClustree_UI()`	plot clustree ui
`plotCoverage()`	Plot Coverage Module
`plotCoverage_UI()`	Title
`plotDimRed()`	Plot Dimensional Reduduction
`plotDimRedui()`	Plot Dimensional Reduduction UI
`plotHeatmap()`	Plot Heatmap
`plotHeatmapui()`	Plot Heatmap ui
`plotReadCount()`	Plot Read Count
`plotReadCountui()`	Plot Read Count UI
`plotViolin()`	Plot Violin Server
`plotViolinui()`	Title
`plot_all_ptimes()`	Plot a Set of Heatmaps Based on a provided pseudotime
`plot_all_transcripts()`	Plot All Transcripts
`plot_cds()`	Plot a Monocle Cell Data Set
`plot_cell_cycle_distribution()`	Plot cell cycle distribution grouped by metadata
`plot_cells()`	Plot cells of a monocle cell data set
`plot_feature()`	Plot Feature
`plot_feature_in_ref_query_ptime()`	Plot Expression of a Given Feature of a set of Pseudotimes
`plot_gene_coverage_by_var()`	Plot BigWig Coverage for Genes of Interest by a Given Variable
`plot_markers()`	Plot Cluster Marker Genes
`plot_monocle_features()`	Plot feature expression on a Monocle Cell Data Set
`plot_multiple_branches_heatmap()`	Plot monocle pseudotime over multiple branches
`plot_pseudotime()`	Plot pseudotime on a Monocle Cell Data Set
`plot_pseudotime_heatmap()`	plot pseudotime heatmap
`plot_readcount()`	Plot Read Count
`plot_scvelo()`	plot scvelo
`plot_transcript_composition()`	Plot Transcript Composition
`plot_var()`	Plot Metadata Variables
`plot_violin()`	Plot Violin plot
`plotly_settings()`	Plotly settings
`prep_armor_meta()`	prep armor metadata file
`prep_plot_genes_in_pseudotime()`	Title
`prep_slider_values()`	Prep Slider Values
`process_monocle_child()`	Preprocess a Monocle v2 object for heatmap based on provided pseudotime
`propagate_spreadsheet_changes()`	Propagate Metadata Changes
`query_experiment()`	Query Assay
`read_project_db()`	Read a database of seuratTools projects
`record_experiment_data()`	Record Experiment Metadata
`reference_integrate()`	Transfer labels between gene or transcript objects
`reformatMetadataDR()`	Reformat Seurat Object Metadata Server
`reformatMetadataDRui()`	Reformat Seurat Object Metadata UI
`regress_by_features()`	Regress Seurat Object by Given Set of Genes
`reintegrate_seu()`	Reintegrate (filtered) seurat objects
`rename_from_x_notation()`	Rename cell ids from annoying old notation
`rename_seurat()`	Give a new project name to a seurat object
`reorg_seurat_files()`	Reorganize seurat objects to a multimodal format
`reset_seu_meta()`	Reset Seurat Metadata
`run_BEAM()`	Run BEAM from Monocle2
`run_census()`	Run Census
`run_enrichmentbrowser()`	Run Enrichment Browser on Differentially Expressed Genes
`run_hmap()`	Run heatmap from Monocle2
`run_seurat_de()`	Run Seurat Differential Expression
`save_seurat()`	Save seurat object to /output/sce/_seu.rds
`sce_from_tibbles()`	Create Single Cell Experiment from Tibbles
`scvelo_expression()`	plot scvelo expression
`set_colnames_txi()`	Set Column Names from `tximport`
`seu_calcn()`	Calculate Read Count Metrics for a Seurat object
`seu_complex_heatmap()`	Plot Annotated Complexheatmap from Seurat object
`seu_from_tibbles()`	Create a Seurat Object from a set of tibbles
`seu_from_tximport()`	Create a seurat object from output of tximport and a table of cell metadata
`seuratApp()`	Create a shiny app for a project on disk
`seuratToolsBox()`	custom collapsible box
`seurat_cluster()`	Run Louvain Clustering at Multiple Resolutions
`seurat_find_markers()`	Find Cell Type Markers in a Seurat Object
`seurat_integrate()`	Batch Correct Multiple Seurat Objects
`seurat_integration_pipeline()`	Run Seurat Integration
`seurat_pipeline()`	Run Seurat Pipeline
`seurat_preprocess()`	Preprocess Seurat Object
`seurat_reduce_dimensions()`	Dimensional Reduction
`seurat_v5_integrate()`	Batch Correct Multiple Seurat Objects
`seurat_v5_integration_pipeline()`	Run Seurat Integration
`stash_marker_features()`	Stash Marker Genes in a Seurat Object
`subset_by_meta()`	Subset by new metadata
`swap_counts_from_feature()`	Swap counts from Feature
`tableSelected()`	Create Table of Selected Cells
`tableSelectedui()`	Create Table of Selected Cells UI
`techInfo()`	Title
`techInfoui()`	Title
`threshold_monocle_genes()`	Threshold monocle genes
`transcripts_to_genes()`	Ensembl Transcript Ids to Gene Symbols
`unite_metadata()`	Unite metadata
`update_exp_meta()`	Update experiment Metadata
`update_human_gene_symbols()`	Update human gene symbols in seurat object
`update_project_db()`	Update a database of seuratTools projects
`update_seu_meta()`	Update Seurat Metadata from Project
`update_seuratTools_object()`	Update a seuratTools Object
`velocyto_assay()`	run velocyto on a gene or transcript level seurat object
`velocyto_seu()`	run velocyto on a seurat object
`velocyto_seurat_from_loom()`	Run RNA Velocity starting with only a loom File

Reference

All functions