An overview of the key functions available in the eccDNAscopeR package

create_eccDNA_obj()

Convert Cell Ranger results into a eccDNA object(Seurat_obj)

perform_QC()

Perform quality control on the generated scATAC data

estimate_Copy_num()

Calculate the number of fragments with copy number amplification in each cell

estimate_Adapter_num()

Calculate the number of adapter(breakpoint) of eccDNA in each cell

estimate_eccDNA_gene_num()

Calculate the number of eccDNA genes in each cell

assign_eccDNA_features()

Assign eccDNA features to the eccDNA(Seurat) object

get_eccDNA_cells()

Select cells eligible for eccDNA visualization from a specific sample.

plot_eccDNAs_in_one_cell()

Visualizing eccDNA in specific cell

plot_single_eccDNA_in_one_cell()

Plot the amplification structure of a single eccDNA-related gene in a specific cell

integrate_eccDNA_amplified_genes()

Integrate eccDNA-related gene amplification information across all samples

plot_eccDNA_amplified_genes()

Plot the relationship between breakpoints and copy numbers of eccDNA-amplified genes

plot_eccDNA_genomic_distribution()

Plot the distribution of eccDNA genomic regions

creat_eccDNA_frame()

Create a data frame to record the copy number information of each eccDNA-related gene in each cell across all samples

creat_eccDNA_clone_obj()

Generate a Seurat object for eccDNA clone analysis

creat_eccDNA_clone_trajectory()

eccDNA clone trajectory analysis

extract_clone_branch()

Extract all sub-paths from the eccDNA clone trajectory plot

plot_clone_branch_features()

Plot a heatmap of genes with significant changes on the clone branches

single_eccDNA_clone_cluster()

Perform hierarchical clustering on cells with amplification of a single eccDNA-related gene

shared_eccDNA_num_between_cells()

Calculate the shared eccDNA gene number between cells

cor_single_eccDNA_clone_cluster()

Compare the similarity between and within groups of cells based on the transcription start site (TSS) enrichment scores of genes in single_eccDNA_clone_cluster