Pipeline for single cell multi-omic data pre-processing
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Documentation for package ‘scPipe’ version 2.4.0
Help Pages
| 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 | Calculate 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 |
| check_barcode_start_position | Check Valid Barcode Start Position |
| 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 |
| feature_info | Get or set 'feature_info' from a SingleCellExperiment object |
| feature_info-method | Get or set 'feature_info' from a SingleCellExperiment object |
| feature_info.sce | Get or set 'feature_info' from a SingleCellExperiment object |
| feature_info<- | Get or set 'feature_info' from a SingleCellExperiment object |
| feature_info<--method | Get or set 'feature_info' from a SingleCellExperiment object |
| feature_type | Get or set 'feature_type' from a SingleCellExperiment object |
| feature_type-method | Get or set 'feature_type' from a SingleCellExperiment object |
| feature_type.sce | Get or set 'feature_type' from a SingleCellExperiment object |
| feature_type<- | Get or set 'feature_type' from a SingleCellExperiment object |
| feature_type<--method | Get or set 'feature_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 |
| 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_chromosomes | Get Chromosomes |
| 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 |
| read_cells | Read Cell barcode file |
| remove_outliers | Remove outliers in 'SingleCellExperiment' |
| scPipe | scPipe - single cell RNA-seq pipeline |
| sc_aligning | aligning the demultiplexed FASTQ reads using the Rsubread:align() |
| sc_atac_bam_tagging | BAM tagging |
| sc_atac_cell_calling | identifying true vs empty cells |
| sc_atac_create_cell_qc_metrics | generating a file useful for producing the qc plots |
| sc_atac_create_fragments | Generating the popular fragments for scATAC-Seq data |
| sc_atac_create_report | HTML report generation |
| sc_atac_create_sce | sc_atac_create_sce() |
| sc_atac_emptydrops_cell_calling | empty drops cell calling |
| sc_atac_feature_counting | generating the feature by cell matrix |
| sc_atac_filter_cell_calling | filter cell calling |
| sc_atac_peak_calling | sc_atac_peak_calling() |
| sc_atac_pipeline | A convenient function for running the entire pipeline |
| sc_atac_pipeline_quick_test | A function that tests the pipeline on a small test sample (without duplicate removal) |
| sc_atac_plot_cells_per_feature | A histogram of the log-number of cells per feature |
| sc_atac_plot_features_per_cell | A histogram of the log-number of features per cell |
| sc_atac_plot_features_per_cell_ordered | Plot showing the number of features per cell in ascending order |
| sc_atac_plot_fragments_cells_per_feature | A scatter plot of the log-number of fragments and log-number of cells per feature |
| sc_atac_plot_fragments_features_per_cell | A scatter plot of the log-number of fragments and log-number of features per cell |
| sc_atac_plot_fragments_per_cell | A histogram of the log-number of fragments per cell |
| sc_atac_plot_fragments_per_feature | A histogram of the log-number of fragments per feature |
| sc_atac_remove_duplicates | Removing PCR duplicates using samtools |
| sc_atac_tfidf | generating the UMAPs for sc-ATAC-Seq preprocessed data |
| sc_atac_trim_barcode | demultiplex raw single-cell ATAC-Seq fastq reads |
| sc_correct_bam_bc | sc_correct_bam_bc |
| 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_get_umap_data | Generates UMAP data from sce object |
| sc_integrate | Integrate multi-omic scRNA-Seq and scATAC-Seq data into a MultiAssayExperiment |
| sc_interactive_umap_plot | Produces an interactive UMAP plot via Shiny |
| sc_mae_plot_umap | Generates UMAP of multiomic data |
| 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 |
| TF.IDF.custom | Returns the TF-IDF normalised version of a binary matrix |
| 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 |