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| scPipe-package | scPipe - single cell RNA-seq pipeline |
| calculate_QC_metrics | Get QC metrics using gene counting matrix |
| cell_barcode_matching | cell barcode demultiplex statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe |
| convert_geneid | convert the gene ids of a SingleCellExperiment object |
| create_report | create_report |
| create_sce_by_dir | create a SingleCellExperiment object from data folder generated by preprocessing step |
| demultiplex_info | demultiplex_info |
| demultiplex_info-method | demultiplex_info |
| demultiplex_info.sce | demultiplex_info |
| demultiplex_info<- | demultiplex_info |
| demultiplex_info<--method | demultiplex_info |
| detect_outlier | Detect outliers based on QC metrics |
| gene_id_type | Get or set 'gene_id_type' from a SingleCellExperiment object |
| gene_id_type-method | Get or set 'gene_id_type' from a SingleCellExperiment object |
| gene_id_type.sce | Get or set 'gene_id_type' from a SingleCellExperiment object |
| gene_id_type<- | Get or set 'gene_id_type' from a SingleCellExperiment object |
| gene_id_type<--method | Get or set 'gene_id_type' from a SingleCellExperiment object |
| get_genes_by_GO | Get genes related to certain GO terms from biomart database |
| organism | Get or set 'organism' from a SingleCellExperiment object |
| organism-method | Get or set 'organism' from a SingleCellExperiment object |
| organism.sce | Get or set 'organism' from a SingleCellExperiment object |
| organism<--method | Get or set 'organism' from a SingleCellExperiment object |
| plot_demultiplex | plot_demultiplex |
| plot_mapping | plot mapping statistics for 'SingleCellExperiment' object. |
| plot_QC_pairs | plot QC statistics for 'SingleCellExperiment' object |
| plot_UMI_dup | plot_UMI_dup |
| QC_metrics | Get or set quality control metrics in a SingleCellExperiment object |
| QC_metrics-method | Get or set quality control metrics in a SingleCellExperiment object |
| QC_metrics.sce | Get or set quality control metrics in a SingleCellExperiment object |
| QC_metrics<- | Get or set quality control metrics in a SingleCellExperiment object |
| QC_metrics<--method | Get or set quality control metrics in a SingleCellExperiment object |
| remove_outliers | remove outliers for 'SingleCellExperiment' |
| scPipe | scPipe - single cell RNA-seq pipeline |
| sc_demultiplex | sc_demultiplex |
| sc_detect_bc | sc_detect_bc |
| sc_exon_mapping | sc_exon_mapping |
| sc_gene_counting | sc_gene_counting |
| sc_sample_data | a small sample scRNA-seq counts dataset to demonstrate capabilities of scPipe |
| sc_sample_qc | quality control information for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe. |
| sc_trim_barcode | sc_trim_barcode |
| UMI_duplication | UMI duplication statistics for a small sample scRNA-seq dataset to demonstrate capabilities of scPipe |
| UMI_dup_info | Get or set UMI duplication results in a SingleCellExperiment object |
| UMI_dup_info-method | Get or set UMI duplication results in a SingleCellExperiment object |
| UMI_dup_info.sce | Get or set UMI duplication results in a SingleCellExperiment object |
| UMI_dup_info<- | Get or set UMI duplication results in a SingleCellExperiment object |
| UMI_dup_info<--method | Get or set UMI duplication results in a SingleCellExperiment object |