Man pages for kidcancerlab/rrrSingleCellUtils
A Set of Tools For Single Cell Analysis
| add_atac_metadata | Add ATAC specific metadata to the Seurat object |
| add_nucleosome_signal | Add nucleosome signal to ATAC data in a Seurat object |
| annotate_atac | Add annotation to ATAC data in a Seurat object |
| annotate_celltypes | Annotate normal human and mouse cells in seurat object. |
| auto_subset | Use median and standard deviation to subset a Seurat object... |
| calc_frip | Calculate FRiP for a Seurat object |
| check_cmd | Check that a command is available on the system |
| feature_hist | Make ggplot2-based histograms of Seurat features |
| find_ligands | Function findLigands |
| find_tar_genes | Create a gene list containing putative targets of ligand... |
| gen_cellecta_bc_data | Extract cellecta barcode information from a sam or bam file |
| gen_lig_receptor_ref | Get reference data for find_ligand() function |
| get_cell_cycle_genes | Get Cell Cycle Genes |
| kill_cc | Regress out cell cycle effects |
| load_lig_receptor_data | Load ligand receptor data |
| merge_atac | Merge multiple ATAC-seq samples into a single Seurat object |
| merge_gex_atac | Merge GEX and ATAC data |
| optimize_silhouette | Find optimal FindClusters() resolution value to maximize... |
| pipe | Pipe operator |
| plot_cc | Plot Cell Cycle Distribution |
| plot_cols | Color scheme to use for plots |
| plot_complex_heatmap | Make a complex heatmap showing nichenet output from... |
| process_ltbc | Process Lineage Tracing Barcodes |
| process_seurat | Process a Seurat object |
| process_seurat_atac | Process a Seurat object with ATAC data |
| r_dim_plot | Roberts lab Seurat::DimPlot default changes |
| r_feature_plot | Roberts lab Seurat::FeaturePlot default changes |
| r_make_loom_files | Wrapper to Make Loom Files in R |
| rrrSingleCellUtils-package | rrrSingleCellUtils: A Set of Tools For Single Cell Analysis |
| run_fdl | Run Force-Directed Layout (FDL) on a Seurat object |
| silhouette_cluster_mean | Calculate the average silhouette score from each cluster in a... |
| silhouette_mean | Calculate the average silhouette score from a silhouette... |
| silhouette_plot | Plot silhouette scores |
| silhouette_seurat | Perform silhouette scoring on a Seurat object. |
| silhouette_to_df | Run silhouette scoring and return a to data frame |
| tenx_load_qc | Load 10X data |
| theme_roberts | Roberts lab ggplot theme defaults |
| tss_enrichment | Calculate TSS enrichment for a Seurat object |
| use_sbatch_template | Use a Sbatch Template to Submit a Job to the Cluster |
| write_off_md | Save Off Metadata for Velocity Analysis |
