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-package          cicero
cicero_data             Example single-cell chromatin accessibility
                        data
compare_connections     Compare Cicero connections to other datasets
df_for_coords           Construct a data frame of coordinate info from
                        coordinate strings
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
