Man pages for SCOPE
A normalization and copy number estimation method for single-cell DNA sequencing
| coverageObj.scopeDemo | Pre-stored coverageObj.scope data for demonstration purposes |
| get_bam_bed | Get bam file directories, sample names, and whole genomic... |
| get_coverage_scDNA | Get read coverage from single-cell DNA sequencing |
| get_gc | Compute GC content |
| get_gini | Compute Gini coefficients for single cells |
| get_mapp | Compute mappability |
| get_samp_QC | Get QC metrics for single cells |
| iCN_sim | A post cross-sample segmentation integer copy number matrix... |
| initialize_ploidy | Ploidy pre-initialization |
| initialize_ploidy_group | Group-wise ploidy pre-initialization |
| normalize_codex2_ns_noK | Normalization of read depth without latent factors under the... |
| normalize_scope | Normalization of read depth with latent factors using... |
| normalize_scope_foreach | Normalization of read depth with latent factors using... |
| normalize_scope_group | Group-wise normalization of read depth with latent factors... |
| normObj.scopeDemo | Pre-stored normObj.scope data for demonstration purposes |
| perform_qc | Quality control for cells and bins |
| plot_EM_fit | Visualize EM fitting for each cell. |
| plot_iCN | Plot post-segmentation copy number profiles of integer values |
| QCmetric.scopeDemo | Pre-stored QCmetric data for demonstration purposes |
| ref.scopeDemo | Pre-stored 500kb-size reference genome for demonstration... |
| ref_sim | A reference genome in the toy dataset |
| segment_CBScs | Cross-sample segmentation |
| Y_sim | A read count matrix in the toy dataset |
