Man pages for cellpypes
Cell Type Pipes for Single-Cell RNA Sequencing Data
| classify | Classify cells on previously defined rules |
| class_to_deseq2 | Create DESeq2 object for a given cell type |
| evaluate_rule | Evaluate rule to obtain positive / negative cells |
| feat | Feature plots: Color gene expression in 2D embeddings |
| find_knn | Find approximate k-nearest neighbors |
| is_classes | Check if obj$classes looks as expected. is_class returns... |
| is_rules | Check if obj$rules looks as expected. |
| knn_refine | Refine cell type labels with knn classifier |
| plot_classes | Call and visualize 'classify' function |
| plot_last | Plot the last modified rule or class |
| pool_across_neighbors | Sum up x across neighbors in a nearest neighbor graph. |
| pseudobulk | Form pseudobulks from single cells. |
| pseudobulk_id | Generate unique IDs to identify your pseudobulks. |
| pype_code_template | Generate code template for cellpype rules |
| pype_from_seurat | Convert Seurat to cellpypes object. |
| rule | Add a cell type rule. |
| simulated_umis | Simulated scRNAseq data |
| tree_ancestry | Find parent, parent's parent and so on for a class using... |
| tree_descendants | Find child, child's child and so on for class(es) using... |
| tree_leaf_nodes | Finds leaf nodes, i.e. classes without children |
