Man pages for cole-trapnell-lab/cicero
Predict cis-co-accessibility from single-cell chromatin accessibility data
| aggregate_by_cell_bin | Aggregate count CDS by groups of cells |
| aggregate_nearby_peaks | Make an aggregate count cds by collapsing nearby peaks |
| annotate_cds_by_site | Add feature data columns to fData |
| assemble_connections | Combine and reconcile cicero models |
| build_gene_activity_matrix | Calculate initial Cicero gene activity matrix |
| cell_data | Metadata for example cells in cicero_data |
| cicero_data | Example single-cell chromatin accessibility data |
| cicero-package | cicero |
| compare_connections | Compare Cicero connections to other datasets |
| df_for_coords | Construct a data frame of coordinate info from coordinate... |
| estimate_distance_parameter | Calculate distance penalty parameter |
| find_overlapping_ccans | Find CCANs that overlap each other in genomic coordinates |
| find_overlapping_coordinates | Find peaks that overlap a specific genomic location |
| gene_annotation_sample | Example gene annotation information |
| generate_ccans | Generate cis-co-accessibility networks (CCANs) |
| generate_cicero_models | Generate cicero models |
| human.hg19.genome | Chromosome lengths from human genome hg19 |
| make_atac_cds | Make ATAC CDS object |
| make_cicero_cds | Create cicero input CDS |
| make_sparse_matrix | Make a symmetric square sparse matrix from data frame |
| normalize_gene_activities | Normalize gene activities |
| plot_accessibility_in_pseudotime | Plot accessibility by pseudotime |
| plot_connections | Plot connections |
| ranges_for_coords | Construct GRanges objects from coordinate strings |
| run_cicero | Run Cicero |
