QC_metrics              Get or set quality control metrics in a
                        SingleCellExperiment object
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    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
detect_outlier          Detect outliers based on QC metrics
gene_id_type            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.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.
remove_outliers         Remove outliers in 'SingleCellExperiment'
scPipe                  scPipe - single cell RNA-seq pipeline
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_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
