API for shahcompbio/signals
Single Cell Genomes with Allele Specificity
| Global functions | |
|---|---|
| %>% | Man page |
| .callHaplotypeSpecificCN_ | Source code |
| CapStr | Source code |
| HaplotypeHMM | Source code |
| Mode | Source code |
| add_gene_locations_to_seurat | Man page |
| alleleHMM | Source code |
| assignHaplotypeHMM | Source code |
| assign_haplotype_label | Source code |
| assign_states_noprior | Source code |
| assignalleleHMM | Source code |
| calc_state_mode | Source code |
| callAlleleSpecificCN | Man page Source code |
| callAlleleSpecificCNfromHSCN | Man page Source code |
| callHaplotypeSpecificCN | Man page |
| callalleleHMMcell | Source code Source code |
| cell_order_from_tree | Source code |
| coord_to_arm | Man page |
| createCNmatrix | Source code |
| createSVmatforhmap | Source code |
| find_largest_contiguous_group | Source code |
| format_clones | Source code |
| format_copynumber | Source code |
| format_copynumber_values | Source code |
| format_haplotypes_dlp | Source code |
| format_tree | Source code |
| getBins | Man page |
| getSVlegend | Source code |
| get_bezier_df_2 | Source code |
| get_cells_per_chr_global | Source code |
| get_chrom_label_pos | Source code |
| get_clone_label_pos | Source code |
| get_clone_members | Source code |
| get_gene_idx | Source code |
| get_genomecoords_label_pos | Source code |
| get_label | Source code |
| get_library_labels | Source code |
| get_ordered_cell_ids | Source code |
| get_states_dna | Source code |
| getstate | Source code |
| hc_clustering | Source code |
| is.ascn | Source code |
| is.hscn | Source code |
| is.hscnrna | Source code |
| logspace_add | Source code |
| logspace_addcpp | Source code |
| make_arm_matrix | Source code |
| make_bottom_annot | Source code |
| make_clone_palette | Source code |
| make_copynumber_heatmap | Source code |
| make_copynumber_legend | Source code |
| make_corrupt_tree_heatmap | Source code |
| make_discrete_palette | Source code |
| make_left_annot | Source code |
| make_left_annot_generic | Source code |
| make_top_annotation_gain | Source code |
| make_top_annotsnv | Source code |
| make_tree_ggplot | Source code |
| min_cells | Source code |
| missegregations | Source code |
| multi.mixedorder | Source code |
| normalize_cell_ploidy | Source code |
| per_chr_baf_plot | Source code |
| per_segment_baf_plot | Source code |
| phase_haplotypes_rna | Source code |
| plotBAFperstate | Man page |
| plotCNprofile | Man page |
| plotCNprofileBAF | Man page |
| plotHeatmap | Man page Source code |
| plotHeatmapBAF | Source code |
| plotSV | Source code |
| plotSV2 | Source code |
| plotSVlines | Source code |
| plot_clusters_used_for_phasing | Man page |
| plot_proportions | Source code |
| plot_umap | Source code |
| plottinglist | Source code |
| plottinglistSV | Source code |
| possible_states_df | Source code |
| print.ascn | Source code |
| print.hscn | Source code |
| print.hscnrna | Source code |
| rephasebins | Man page |
| scBAFstate_cols | Source code |
| scCN_cols | Source code |
| scCN_pal | Source code |
| scCNminorallele_cols | Source code |
| scCNphase_cols | Source code |
| scCNstate_cols | Source code |
| scale_color_scCN | Man page Source code |
| scale_fill_scCN | Man page Source code |
| simulate_cell | Source code |
| space_copynumber_columns | Source code |
| squashy_trans | Source code |
| switch_alleles | Source code |
| umap_clustering | Man page Source code |
| umap_clustering_breakpoints | Source code |
| viterbi | Source code |
| viterbiR | Source code |
