# Predict cis-co-accessibility from single-cell chromatin accessibility data

## Documentation for package ‘cicero’ version 1.30.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

cicero-package | cicero
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 | 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
generate_ccans | Generate cis-co-accessibility networks (CCANs)
generate_cicero_models | Generate cicero models
gene_annotation_sample | Example gene annotation information
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