.qq_outliers_robust     Detect outliers based on robust linear
                        regression of QQ plot
QC_metrics              Get or set quality control metrics in a
                        SingleCellExperiment object
TF.IDF.custom           Returns the TF-IDF normalised version of a
                        binary matrix
UMI_dup_info            Get or set UMI duplication results in a
                        SingleCellExperiment object
UMI_duplication         UMI duplication statistics for a small sample
                        scRNA-seq dataset to demonstrate capabilities
                        of scPipe
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
detect_outlier          Detect outliers based on QC metrics
feature_info            Get or set 'feature_info' from a
                        SingleCellExperiment object
feature_type            Get or set 'feature_type' from a
                        SingleCellExperiment object
gene_id_type            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.sce            Get or set 'organism' from a
                        SingleCellExperiment object
plot_QC_pairs           Plot GGAlly pairs plot of QC statistics from
                        'SingleCellExperiment' object
plot_UMI_dup            Plot UMI duplication frequency
plot_demultiplex        plot_demultiplex
plot_mapping            Plot mapping statistics for
                        '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
