Man pages for OliverDietrich/SeuratHelper
Helper functions to assist scRNA-seq data analysis from a Seurat object
| AddAUC | Calculate AUC for marker list |
| add_qc_metrics | Add QC metrics |
| annotate_maxAUC | Annotate clusters based on maximum AUC score |
| combinations | Paste columns of a data.frame into a vector |
| convert_names | Convert feature names |
| from_sce | Convert from SingleCellExperiment to Seurat |
| heatmap_expression | Create heatmap of gene expression |
| minmax | Minmax scaling for numeric vector |
| plot_association | Plot association between cell data |
| plot_embedding | Plot low-dimensional cell embedding |
| plot_markers_embedding | Plot cell type markers on embedding |
| plot_qc_metrics | Plot QC metrics |
| read_h5ad | Read anndata object (.h5ad) and convert to Seurat object on... |
| read_layer_h5ad | Get layer from AnnData |
| read_obsm_h5ad | Read obsm from AnnData |
| read_slot_h5ad | Get slot from AnnData |
| RunMNN | Perform Mutual Nearest Neighbor Integration |
| select_most_frequent_category | Select maximum occuring category in vector |
| summarize_groups | Summarize groups of columns in a matrix |
| summarize_overlapping_rows | Summarize rows that have overlapping coordinates |
| test_diffexp | Test differential expression |
| to_sce | Convert from Seurat to SingleCellExperiment |
| unique_combinations | Create unique combinations from a data.frame of factors |
| violin_expression | Create violin plot of gene expression |
| which_rowMax | Extract the column names of row maxima |
| write_h5ad | Convert Seurat to h5ad |
