Man pages for whtns/seuratTools
Tools for Managing Seurat Objects
| 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... |
| 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_seurat_to_sce | convert seurat object to cds |
| convert_seu_to_cds | Convert a Seurat Object to a Monocle Cell Data Set |
| 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_to_h5ad | convert a seurat object to an on-disk anndata object |
| convert_v3_to_v5 | Convert seurat object to seurat V5 format |
| create_project_db | Create a database of seuratTools projects |
| create_proj_matrix | Create a Table of single Cell 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 |
| dot-send_enrichr_query | Gene enrichment using Enrichr. |
| dropdownButton | Custom Dropdown Button |
| 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 |
| find_all_markers | Find All Markers |
| findMarkers | Find Markers |
| findMarkersui | Find Markers UI |
| flip_pseudotime | Flip Pseudotime |
| format_new_metadata | Add Seurat Object Metadata |
| format_pathway_table | Title |
| genes_to_transcripts | Gene Symbols to Ensembl Transcript Ids |
| gene_test_plot | Plot Gene expression over pseudotime on reference and query... |
| 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_small_seus | Merge Small Seurat Objects |
| metadata_from_batch | Retrieve Metadata from Batch |
| minimalSeuratApp | Create a minimal seurat app |
| monocle | Monocle Server Module |
| Monocle2_diffex | Monocle2 differential expression |
| monocle_module_heatmap | Title |
| monocleui | Monocle UI Module |
| nil | nil operator |
| pad_sample_files | pad sample numbers to prep for armor |
| pathwayEnrichment | pathway enrichment |
| pathwayEnrichmentui | Title |
| pipe | Pipe operator |
| 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 |
| 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 |
| 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... |
| plotHeatmap | Plot Heatmap |
| plotHeatmapui | Plot Heatmap ui |
| plotly_settings | Plotly settings |
| 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 |
| plotReadCount | Plot Read Count |
| plotReadCountui | Plot Read Count UI |
| plot_scvelo | Plot scvelo on embedding plot |
| plot_transcript_composition | Plot Transcript Composition |
| plot_var | Plot Metadata Variables |
| plotVelocity | RNA Velocity Server Module |
| plotVelocityui | RNA Velocity UI Module |
| plot_violin | Plot Violin plot |
| plotViolin | Plot Violin Server |
| plotViolinui | Title |
| prep_armor_meta | prep armor metadata file |
| prep_plot_genes_in_pseudotime | Title |
| prep_scvelo | scvelo_assay |
| prep_slider_values | Prep Slider Values |
| process_monocle_child | Preprocess a Monocle v2 object for heatmap based on provided... |
| propagate_spreadsheet_changes | Propagate Metadata Changes |
| 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_scvelo | scvelo_assay |
| 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 |
| set_colnames_txi | Set Column Names from 'tximport' |
| SetDefaultAssay | Reset default assay |
| 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... |
| seuratApp | Create a shiny app for a project on disk |
| 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 |
| seuratToolsBox | custom collapsible box |
| 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 |
