Man pages for Chris-Cherry/sctools
Single cell analysis tools package
| align_sers | Aligns a list of ser objects |
| average_scores | Average matrix by metadata |
| Bclone_processing | Process B cell clonality |
| clust_proportions | Creates cluster proportions and plots from metadata. |
| convert_genes | Convert genes between symbol types |
| ggplot_col_gen | Generate ggplot colors |
| label_transfer | Transfers labels from reference data to query data |
| make_de_plots | Runs differential expression and creates relevant plots for a... |
| make_gse_scores | Makes gene set enrichment scores by cell |
| make_processing_plots | Make default plot array associated with processing step. |
| make_tar_feat_plots | Make violin and feature plots for a given set of features |
| organize_scores | Sort matrix by Seurat metadata |
| process_B | This function integrates B cell data vdj sequence into the... |
| process_counts_hash | Processes counts into a Seurat object prepared for alignment. |
| process_loom | Reads in loom files for rnavel_plot.R |
| process_ser | Processes counts into a Seurat object prepared for alignment. |
| process_T | Processes_T: This function integrate T cell data with alpha... |
| pseudotime_plot | Creates pseudotime |
| pseudotime_plot3d | Generate flashing and spinning 3d pseudotime plots |
| rank_gse | This function will perform fast preranked gene set... |
| ref_ser_process | Processes counts into a Seurat object prepared for alignment... |
| rnavel_plot | Creates an RNA velocity projection |
| run_de | Runs differential expression for a ser object |
| scn_prediction | singleCellNet training and prediction |
| signed_set_scoring | Scores cell expression of genes in set taking into account... |
| Tclone_processing | This file process T cell clonality. |
