Man pages for crhisto/SCDC
Bulk RNA-seq deconvolution by scRNA-seq with multi-reference datasets
| bootstrap_gene_finder | Function that perform a boostrap process from one cluster... |
| calculate_foldchange | Function that calculates the foldchange between a given... |
| calculate_genes_using_dbscan | Function that selects the markers genes given a wilcox object... |
| CreateSCDCpropObj | Create user-defined SCDC_prop object, as the SCDC_ENSEMBLE... |
| custom_apply | custom_apply Function |
| DemoPlot | Demographic figure for single cells |
| generateBulk_allcells | Construct Pseudo bulk samples |
| generateBulk_norep | Construct Pseudo bulk samples - random |
| getCPM0 | Normalize matrix / vector |
| getESET | Get ExpressionSet |
| getSearchGrid | Grid search matrix |
| iteration_over_clusters_default_parallelized | parallelization of the for the original procedure with some... |
| iteration_over_clusters_parallelized | Paralellization of the for procedure for QC process |
| iteration_over_clusters_parallelized_wilcox | Marker gene selection with parallelization using wilcox... |
| iteration_over_clusters_parallelized_wilcox_boostrap | Marker gene selection with parallelization using wilcox... |
| save_log_file | Function to save message in a log file for each loop: |
| SCDC_basis | Basis Matrix |
| SCDC_basis_ONE | Basis matrix for single cells from one subject |
| SCDC_ENSEMBLE | ENSEMBLE function |
| SCDC_peval | Evaluate deconvolved proportions |
| SCDC_prop | Proportion estimation |
| SCDC_prop_ONE | Proportion estimation function for one-subject case |
| SCDC_prop_ONE_subcl_marker | Tree-guided proportion estimation for ONE subject |
| SCDC_prop_subcl_marker | Tree-guided proportion estimation |
| SCDC_qc | Clustering QC |
| SCDC_qc_ONE | Clustering QC for single cells from one subject |
| SCDC_yeval | Evaluate predicted gene expression levels |
| wheat_map | Heatmap for ENSEMBL weight selection, with four measures |
| wt_prop | Calculate cell type proportions by suggested weights |
| wt_y | Calculate cell type proportions by suggested weights |
