API for cole-trapnell-lab/cicero-release
Predict cis-co-accessibility from single-cell chromatin accessibility data
| Global functions | |
|---|---|
| CustomTrack | Source code |
| agg_cells | Source code |
| aggregate_by_cell_bin | Man page Source code |
| aggregate_nearby_peaks | Man page Source code |
| annotate_cds_by_site | Man page Source code |
| assemble_connections | Man page Source code |
| build_composite_gene_activity_matrix | Source code |
| build_gene_activity_matrix | Man page Source code |
| cell_data | Man page |
| cicero | Man page |
| cicero-package | Man page |
| cicero_data | Man page |
| compare_connections | Man page Source code |
| df_for_coords | Man page Source code |
| estimateSizeFactorsSimp | Source code |
| estimate_distance_parameter | Man page Source code |
| estimate_sf_dense | Source code |
| estimate_sf_sparse | Source code |
| find_overlapping_ccans | Man page |
| find_overlapping_coordinates | Man page Source code |
| gene_annotation_sample | Man page |
| generate_ccans | Man page |
| generate_cicero_models | Man page Source code |
| generate_plotting_subset | Source code |
| generate_windows | Source code |
| get_colors | Source code |
| human.hg19.genome | Man page |
| is_chr | Source code |
| is_color | Source code |
| make_atac_cds | Man page Source code |
| make_bin_col | Source code |
| make_cicero_cds | Man page Source code |
| make_gene_model_track | Source code |
| make_peak_track | Source code |
| make_sparse_matrix | Man page Source code |
| monocle_theme_opts | Source code |
| normalize_gene_activities | Man page Source code |
| plotBedpe | Source code |
| plot_accessibility_in_pseudotime | Man page Source code |
| plot_connections | Man page Source code |
| plotpair | Source code |
| ranges_for_coords | Man page Source code |
| reconcile | Source code |
| run_cicero | Man page Source code |
| sparse_to_datatable | Source code |
| split_peak_names | Source code |
