# Pipeline for single cell multi-omic data pre-processing

## Documentation for package ‘scPipe’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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_fragments_cpp | 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