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

Documentation for package ‘cicero’ version 1.16.2

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