Man pages for byzhang23/TreeCorTreat
Tree-based correlation screen for phenotype-associated transcriptomic features and cell types
| access_data_seurat | Extract cell-level meta data and count matrix from Seurat... |
| cancor_permute | Calculate summary statistic and perform permutation test |
| construct_pseudobulk | Construct sample-level pseudobulk gene expression matrix |
| ctprop_cancor | Core function for running treecor_ctprop() pipeline. |
| expr_cancor | Compute summary statistic based on gene expression features |
| extract_hrchy_seurat | Extract hierarchy from Seurat object (Data-driven approach) |
| extract_hrchy_string | Extract hierarchy from a string (based on prior knowledge) |
| extract_PC | Extract top n PCs |
| integrated_cellmeta | Filtered cell-level metadata after data integration |
| modify_label | Modify label for tree nodes |
| raw_data | Raw data for TreeCorTreat package |
| select_hvgs | Select highly variable genes (HVGs) |
| treecor_celldensityplot | Plot kernel density of cells in a UMAP embedding per group |
| treecor_ctprop | Pipeline for TreeCorTreat using celltype proportion as... |
| treecor_deg | Differential gene expression (DGE) analysis |
| treecor_degheatmap | Plot heatmap for top n differentially expressed genes |
| treecor_expr | Pipeline for TreeCorTreat using gene expression as features |
| treecor_harmony | Harmony Integration |
| treecor_samplepcaplot | Sample PCA plot |
| treecortreatplot | Visualize TreeCorTreat |
