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| scPipe-package | scPipe - single cell RNA-seq pipeline |
| .qq_outliers_robust | Detect outliers based on robust linear regression of QQ plot |
| anno_import | Import gene annotation |
| anno_to_saf | Convert annotation from GenomicRanges to Simple Annotation Format (SAF) |
| calculate_QC_metrics | Calcuate QC metrics from gene count 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_processed_report | create_processed_report |
| 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_ercc_anno | Get ERCC annotation table |
| get_genes_by_GO | Get genes related to certain GO terms from biomart database |
| get_read_str | Get read structure for particular scRNA-seq protocol |
| 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 GGAlly pairs plot of QC statistics from 'SingleCellExperiment' object |
| plot_UMI_dup | Plot UMI duplication frequency |
| 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 in 'SingleCellExperiment' |
| scPipe | scPipe - single cell RNA-seq pipeline |
| sc_count_aligned_bam | sc_count_aligned_bam |
| sc_demultiplex | sc_demultiplex |
| sc_demultiplex_and_count | sc_demultiplex_and_count |
| 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 |