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


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Documentation for package ‘cicero’ version 1.12.0

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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