Man pages for seasoncloud/Alleloscope
Allele-specific copy number genotyping for single cell sequencing data
| AssignClones_ref | Using marker regions to assign each cell into c reference... |
| Cov_value | Normalize coverage using identified/ specified normal cells... |
| Createobj | Generate Alleloscope object for analysis |
| EM | Iterative phasing and theta_hat estimation |
| Est_regions | Perform EM iterations on the filtered cells with barcodes,... |
| Genotype | Genotype each cell for each region and plot the genotypes. |
| genotype_conf | Compute confidence scores based on posterior probability for... |
| Genotype_value | Normalize coverage using identified/ specified normal cells... |
| Lineage_plot | Generate genotype plot (scatter plot) for each region and... |
| Matrix_filter | Filter object based on cell number for each SNP, SNP number... |
| plot_scATAC_cnv | Generate Alleloscope object for analysis |
| Rundf_dna | Run all steps for scDNA-seq data |
| Segmentation | HMM segmentation based on coverage matrix for paired tumor... |
| Segments_filter | Select the segments in the "seg_table" with more than nSNP |
| Select_normal | Identify candidate normal cells and normal regions for cell... |
