Man pages for cicero
Precict cis-co-accessibility from single-cell chromatin accessibility data

aggregate_by_cell_binAggregate count CDS by groups of cells
aggregate_nearby_peaksMake an aggregate count cds by collapsing nearby peaks
annotate_cds_by_siteAdd feature data columns to fData
assemble_connectionsCombine and reconcile cicero models
build_gene_activity_matrixCalculate initial Cicero gene activity matrix
cell_dataMetadata for example cells in cicero_data
cicero_dataExample single-cell chromatin accessibility data
compare_connectionsCompare Cicero connections to other datasets
df_for_coordsConstruct a data frame of coordinate info from coordinate...
estimate_distance_parameterCalculate distance penalty parameter
find_overlapping_ccansFind CCANs that overlap each other in genomic coordinates
find_overlapping_coordinatesFind peaks that overlap a specific genomic location
gene_annotation_sampleExample gene annotation information
generate_ccansGenerate cis-co-accessibility networks (CCANs)
generate_cicero_modelsGenerate cicero models
human.hg19.genomeChromosome lengths from human genome hg19
make_atac_cdsMake ATAC CDS object
make_cicero_cdsCreate cicero input CDS
make_sparse_matrixMake a symmetric square sparse matrix from data frame
normalize_gene_activitiesNormalize gene activities
plot_accessibility_in_pseudotimePlot accessibility by pseudotime
plot_connectionsPlot connections
ranges_for_coordsConstruct GRanges objects from coordinate strings
run_ciceroRun Cicero
cicero documentation built on June 17, 2020, 2 a.m.