API for maehrlab/thymusatlastools
Tools for analysis of single-cell transcriptomic data
| Global functions | |
|---|---|
| .onLoad | Source code |
| AvailableData | Man page Source code |
| Capitalize | Source code |
| ClusterBag | Man page Source code |
| ClusterBagStability | Man page Source code |
| DESummaryFast | Man page Source code |
| ExploreIteratively | Man page Source code |
| FetchDataZeroPad | Man page Source code |
| FillNA | Man page Source code |
| FindMarkersFlex | Man page |
| KMeansGapStat | Man page Source code |
| ProjectCells | Man page Source code |
| RefineVariableGenes | Man page Source code |
| SanitizeGenes | Man page |
| SeuratMerge | Man page Source code |
| SeuratPie | Man page Source code |
| SubsetDataFlex | Man page Source code |
| TACS | Man page |
| add_cc_score | Man page Source code |
| add_maehrlab_metadata | Man page Source code |
| add_pseudotime_to_seurat | Man page Source code |
| add_quadrants | Man page |
| add_rp_mt_percentage | Man page Source code |
| add_rp_percentage | Man page Source code |
| add_tcr | Man page Source code |
| aggregate_nice | Man page Source code |
| align_embedding_to_reference | Man page Source code |
| annot_ident_plot | Man page Source code |
| are_compatible | Man page Source code |
| atae | Source code |
| atat | Source code |
| call_monocle_on_seurat | Man page Source code |
| check_xist_all | Man page Source code |
| check_xist_pure | Man page Source code |
| classify_mlr | Man page Source code |
| cluster_summary | Source code |
| cluster_wrapper | Man page Source code |
| collapse_by_name | Man page Source code |
| compare_views | Source code |
| convert_species_dge | Man page Source code |
| custom.make.unique | Man page Source code |
| custom_feature_plot | Man page Source code |
| dendrogram_merge_points | Man page Source code |
| deseuratify_raw_data | Man page Source code |
| dge_merge_list | Man page Source code |
| dir.create.nice | Man page Source code |
| distance_sq | Source code |
| div_by_max | Source code |
| div_by_sum | Source code |
| do_dim_red | Source code |
| do_enrichr | Man page Source code |
| down_idx | Source code |
| expected_doublet_counts | Man page Source code |
| explore_embeddings | Man page Source code |
| export_from_seurat | Man page Source code |
| facet_plot_gene_clusters | Man page Source code |
| faceted_tsne | Man page Source code |
| factor_numeric | Source code |
| fix_cluster_order | Man page Source code |
| flip_table | Source code |
| get_cTEC_mTEC_genes | Man page Source code |
| get_classifier_coefs | Man page Source code |
| get_macosko_cc_genes | Man page Source code Source code |
| get_metadata | Man page Source code |
| get_mouse_tfs | Man page Source code Source code |
| get_ortholog | Man page Source code |
| get_ortholog_nonvec | Man page Source code |
| get_ortholog_table | Man page Source code Source code |
| get_poised_genes | Man page Source code Source code |
| get_preimage | Man page Source code |
| get_ramilowski | Man page Source code Source code |
| get_rene_markers | Man page Source code Source code |
| get_similar_genes | Man page Source code |
| harmonize_species | Man page Source code |
| has_ortholog | Man page Source code |
| heatmap_gene_clusters | Man page Source code |
| is_mt | Man page Source code |
| is_rp | Man page Source code |
| knn_classifier | Man page Source code |
| load_thymus_profiling_data | Man page Source code |
| make_heatmap_for_table | Man page Source code |
| master_pt | Man page Source code |
| matrixify_preserving_rownames | Source code |
| misc_summary_info | Man page Source code |
| multiplot | Source code |
| na2zero | Source code |
| nnz | Source code |
| normalize_cpx_amt | Man page Source code |
| outlier_labeled_scatterplot | Man page Source code |
| pc_as_pt | Man page Source code |
| percentify | Source code |
| plot_dendro_with_rect | Man page Source code |
| prop_nz | Source code |
| remove_TEC_doublets | Man page Source code |
| remove_species_specific_genes | Man page Source code |
| replace_with_int_rank | Man page Source code |
| save_complexity_plot | Source code |
| save_depth_stats | Man page Source code |
| save_feature_plots | Man page Source code |
| save_marker_table | Man page Source code |
| save_plot_grid | Source code |
| screen_receptor_ligand | Source code |
| seuratify_thy_data | Man page Source code |
| smooth_and_cluster_genes | Man page Source code |
| standardize | Source code |
| strip_suffix | Man page Source code |
| strsplit_drop | Man page Source code |
| text2file | Man page Source code |
| time_series | Man page Source code |
| time_series_save | Man page Source code |
| top_genes_by_pc | Source code |
| top_n_preserve_rownames | Source code |
| train_save_classifier | Man page Source code |
| tsne_colored | Man page Source code |
| var_gene_select | Source code |
| vectorize_preserving_rownames | Source code |
| wheel_plot | Man page Source code |
