scPipe-package	scPipe
.qq_outliers_robust	dot-qq_outliers_robust
anno_import	anno_import
anno_to_saf	anno_to_saf
calculate_QC_metrics	calculate_QC_metrics
cell_barcode_matching	cell_barcode_matching
check_barcode_start_position	check_barcode_start_position
convert_geneid	convert_geneid
create_processed_report	create_processed_report
create_report	create_report
create_sce_by_dir	create_sce_by_dir
demultiplex_info	demultiplex_info
demultiplex_info,SingleCellExperiment-method	demultiplex_info
demultiplex_info.sce	demultiplex_info
demultiplex_info<-	demultiplex_info
demultiplex_info<-,SingleCellExperiment-method	demultiplex_info
detect_outlier	detect_outlier
feature_info	feature_info
feature_info,SingleCellExperiment-method	feature_info
feature_info.sce	feature_info
feature_info<-	feature_info
feature_info<-,SingleCellExperiment-method	feature_info
feature_type	feature_type
feature_type,SingleCellExperiment-method	feature_type
feature_type.sce	feature_type
feature_type<-	feature_type
feature_type<-,SingleCellExperiment-method	feature_type
gene_id_type	gene_id_type
gene_id_type,SingleCellExperiment-method	gene_id_type
gene_id_type.sce	gene_id_type
gene_id_type<-	gene_id_type
gene_id_type<-,SingleCellExperiment-method	gene_id_type
get_chromosomes	get_chromosomes
get_ercc_anno	get_ercc_anno
get_genes_by_GO	get_genes_by_GO
get_read_str	get_read_str
organism	organism
organism,SingleCellExperiment-method	organism
organism.sce	organism
organism<-,SingleCellExperiment-method	organism
plot_demultiplex	plot_demultiplex
plot_mapping	plot_mapping
plot_QC_pairs	plot_QC_pairs
plot_UMI_dup	plot_UMI_dup
QC_metrics	QC_metrics
QC_metrics,SingleCellExperiment-method	QC_metrics
QC_metrics.sce	QC_metrics
QC_metrics<-	QC_metrics
QC_metrics<-,SingleCellExperiment-method	QC_metrics
read_cells	read_cells
remove_outliers	remove_outliers
scPipe	scPipe
sc_aligning	sc_aligning
sc_atac_bam_tagging	sc_atac_bam_tagging
sc_atac_cell_calling	sc_atac_cell_calling
sc_atac_create_cell_qc_metrics	sc_atac_create_cell_qc_metrics
sc_atac_create_fragments	sc_atac_create_fragments
sc_atac_create_report	sc_atac_create_report
sc_atac_create_sce	sc_atac_create_sce
sc_atac_emptydrops_cell_calling	sc_atac_emptydrops_cell_calling
sc_atac_feature_counting	sc_atac_feature_counting
sc_atac_filter_cell_calling	sc_atac_filter_cell_calling
sc_atac_peak_calling	sc_atac_peak_calling
sc_atac_pipeline	sc_atac_pipeline
sc_atac_pipeline_quick_test	sc_atac_pipeline_quick_test
sc_atac_plot_cells_per_feature	sc_atac_plot_cells_per_feature
sc_atac_plot_features_per_cell	sc_atac_plot_features_per_cell
sc_atac_plot_features_per_cell_ordered	sc_atac_plot_features_per_cell_ordered
sc_atac_plot_fragments_cells_per_feature	sc_atac_plot_fragments_cells_per_feature
sc_atac_plot_fragments_features_per_cell	sc_atac_plot_fragments_features_per_cell
sc_atac_plot_fragments_per_cell	sc_atac_plot_fragments_per_cell
sc_atac_plot_fragments_per_feature	sc_atac_plot_fragments_per_feature
sc_atac_remove_duplicates	sc_atac_remove_duplicates
sc_atac_tfidf	sc_atac_tfidf
sc_atac_trim_barcode	sc_atac_trim_barcode
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	sc_get_umap_data
sc_integrate	sc_integrate
sc_interactive_umap_plot	sc_interactive_umap_plot
sc_mae_plot_umap	sc_mae_plot_umap
sc_sample_data	sc_sample_data
sc_sample_qc	sc_sample_qc
sc_trim_barcode	sc_trim_barcode
TF.IDF.custom	TF.IDF.custom
UMI_duplication	UMI_duplication
UMI_dup_info	UMI_dup_info
UMI_dup_info,SingleCellExperiment-method	UMI_dup_info
UMI_dup_info.sce	UMI_dup_info
UMI_dup_info<-	UMI_dup_info
UMI_dup_info<-,SingleCellExperiment-method	UMI_dup_info
