Man pages for dravishays/scandal
A framework for single-cell analysis
| center_matrix | Centers a matrix |
| compute_complexity | Compute cell complexity |
| load_dataset | Load dataset from file |
| log_transform | Log-transforms a numeric object |
| PreprocConfig-class | PreprocConfig class |
| PreprocConfig-generics | PreprocConfig generics |
| preprocess_matrix | Matrix preprocessing |
| QCResults-class | QCResults class |
| QCResults-generics | QCResults generics |
| scandal | scandal: a package for single-cell analysis |
| scandal_cell_complexity_distribution_plot | Complexity distribution plot |
| scandal_cluster_markers_density | Compute cluster markers density |
| scandal_cna_classify_scores | Classify CNA scores |
| scandal_cna_compute_matrix | CNA matrix computation |
| scandal_cna_compute_scores | Compute the cell CNA score |
| scandal_cna_infer | CNA inference |
| scandal_complexity_distribution_plot | Plot compexity distribution accross different nodes |
| ScandalDataSet | ScandalDataSet class |
| ScandalDataSet-generics | ScandalDataSet generics |
| SCANDAL_G1S_MARKERS | List of G1S cell-cycle markers |
| SCANDAL_G2M_MARKERS | List of G2M cell-cycle markers |
| scandal_histogram_plot | Create a histogram plot |
| SCANDAL_HOUSEKEEPING_GENES_LIST | List of housekeeping genes |
| SCANDAL_IDH_A_AC_MARKERS | List of AC programs markers from IDH-A dataset (Astrocytoma) |
| SCANDAL_IDH_A_G1S_MARKERS | List of G1S (cell cycle) programs markers from IDH-A dataset... |
| SCANDAL_IDH_A_G2M_MARKERS | List of G2M (cell cycle) programs markers from IDH-A dataset... |
| SCANDAL_IDH_A_OC_MARKERS | List of OC programs markers from IDH-A dataset (Astrocytoma) |
| SCANDAL_IDH_A_STEMNESS_MARKERS | List of Stemness programs markers from IDH-A dataset... |
| SCANDAL_IDH_O_AC_MARKERS | List of AC programs markers from IDH-O dataset... |
| SCANDAL_IDH_O_G1S_MARKERS | List of G1S (cell cycle) programs markers from IDH-O dataset... |
| SCANDAL_IDH_O_G2M_MARKERS | List of G2M (cell cycle) programs markers from IDH-O dataset... |
| SCANDAL_IDH_O_OC_MARKERS | List of OC programs markers from IDH-O dataset... |
| SCANDAL_IDH_O_STEMNESS_MARKERS | List of Stemness programs markers from IDH-O dataset... |
| scandal_inspect_samples | Samples inspection |
| scandal_load_data | Loads an RDS file from the file system |
| SCANDAL_MACROPHAGE_MARKERS | List of macrophage markers |
| scandal_mean_expression_frequency_plot | Mean gene expression distribution plot |
| scandal_mean_housekeeping_expression_plot | Housekeeping genes expression plot |
| SCANDAL_OLIGODENDROCYTE_MARKERS | List of oligodendrocyte markers |
| scandal_plot | Plot and save a figure |
| scandal_plot_qc_metrics | Plot quality control metrics |
| scandal_preprocess | Scandal object preprocessing |
| scandal_programs_of_intra_sample_heterogeneity | Programs of intra-sample heterogeneity |
| scandal_quality_control_stats | Quality control statistics |
| scandal_reduced_dims_plot | Create a reduced dimensions plot |
| scandal_save_data | Saves a data object as an RDS file |
| scandal_scatter_plot | Create a scatter plot |
| scandal_setup_analysis | Setup analysis tools |
| scandal_tsne_plot | Create a t-SNE plot |
| scandal_umap_plot | Create a UMAP plot |
| scandal_whiskers_plot | Create a box-and-whiskers plot |
