API for LuyiTian/scPipe
Pipeline for single cell multi-omic data pre-processing

Global functions
.guess_attr	Source code
.onAttach	Source code
.qq_outliers_robust	Man page Source code
QC_metrics	Man page
QC_metrics,SingleCellExperiment-method	Man page
QC_metrics.sce	Man page Source code
QC_metrics<-	Man page
QC_metrics<-,SingleCellExperiment-method	Man page
TF.IDF.custom	Man page Source code
UMI_dup_info	Man page
UMI_dup_info,SingleCellExperiment-method	Man page
UMI_dup_info.sce	Man page Source code
UMI_dup_info<-	Man page
UMI_dup_info<-,SingleCellExperiment-method	Man page
UMI_duplication	Man page
anno_import	Man page Source code
anno_to_saf	Man page Source code
calculate_QC_metrics	Man page Source code
cell_barcode_matching	Man page
check_barcode_reads	Source code
check_barcode_start_position	Man page Source code
convert_geneid	Man page Source code
create_processed_report	Man page Source code
create_report	Man page Source code
create_sce_by_dir	Man page Source code
demultiplex_info	Man page
demultiplex_info,SingleCellExperiment-method	Man page
demultiplex_info.sce	Man page Source code
demultiplex_info<-	Man page
demultiplex_info<-,SingleCellExperiment-method	Man page
detect_outlier	Man page Source code
feature_info	Man page
feature_info,SingleCellExperiment-method	Man page
feature_info.sce	Man page Source code
feature_info<-	Man page
feature_info<-,SingleCellExperiment-method	Man page
feature_type	Man page
feature_type,SingleCellExperiment-method	Man page
feature_type.sce	Man page Source code
feature_type<-	Man page
feature_type<-,SingleCellExperiment-method	Man page
gene_id_type	Man page
gene_id_type,SingleCellExperiment-method	Man page
gene_id_type.sce	Man page Source code
gene_id_type<-	Man page
gene_id_type<-,SingleCellExperiment-method	Man page
get_all_TSS_bins	Source code
get_chromosomes	Man page Source code
get_ercc_anno	Man page Source code
get_genes_by_GO	Man page Source code
get_read_str	Man page Source code
infer_gene_id_from_dbx	Source code
infer_gene_id_from_parent	Source code
infer_gene_ids	Source code
organism	Man page
organism,SingleCellExperiment-method	Man page
organism.sce	Man page Source code
organism<-,SingleCellExperiment-method	Man page
plot_QC_pairs	Man page Source code
plot_UMI_dup	Man page Source code
plot_demultiplex	Man page Source code
plot_mapping	Man page Source code
rcpp_append_chr_to_bed_file	Source code
rcpp_fasta_bin_bed_file	Source code
rcpp_sc_atac_bam_tagging	Source code
rcpp_sc_atac_trim_barcode	Source code
rcpp_sc_atac_trim_barcode_paired	Source code
rcpp_sc_clean_bam	Source code
rcpp_sc_demultiplex	Source code
rcpp_sc_detect_bc	Source code
rcpp_sc_exon_mapping	Source code
rcpp_sc_exon_mapping_df_anno	Source code
rcpp_sc_gene_counting	Source code
rcpp_sc_trim_barcode_paired	Source code
read_cells	Man page Source code
remove_outliers	Man page Source code
scPipe	Man page
scPipe-package	Man page
sc_aligning	Man page
sc_atac_bam_tagging	Man page Source code
sc_atac_cell_calling	Man page Source code
sc_atac_create_cell_qc_metrics	Man page Source code
sc_atac_create_fragments	Man page Source code
sc_atac_create_fragments_cpp	Source code
sc_atac_create_report	Man page Source code
sc_atac_create_sce	Man page Source code
sc_atac_emptydrops_cell_calling	Man page Source code
sc_atac_feature_counting	Man page Source code
sc_atac_filter_cell_calling	Man page Source code
sc_atac_getOverlaps_read2AnyRegion	Source code
sc_atac_getOverlaps_tss2Reads	Source code
sc_atac_peak_calling	Man page Source code
sc_atac_pipeline	Man page Source code
sc_atac_pipeline_quick_test	Man page Source code
sc_atac_plot_cells_per_feature	Man page Source code
sc_atac_plot_features_per_cell	Man page Source code
sc_atac_plot_features_per_cell_ordered	Man page Source code
sc_atac_plot_fragments_cells_per_feature	Man page Source code
sc_atac_plot_fragments_features_per_cell	Man page Source code
sc_atac_plot_fragments_per_cell	Man page Source code
sc_atac_plot_fragments_per_feature	Man page Source code
sc_atac_remove_duplicates	Man page Source code
sc_atac_tfidf	Man page Source code
sc_atac_trim_barcode	Man page Source code
sc_correct_bam_bc	Man page Source code
sc_count_aligned_bam	Man page Source code
sc_demultiplex	Man page Source code
sc_demultiplex_and_count	Man page Source code
sc_detect_bc	Man page Source code
sc_exon_mapping	Man page Source code
sc_gene_counting	Man page Source code
sc_get_umap_data	Man page Source code
sc_integrate	Man page Source code
sc_interactive_umap_plot	Man page Source code
sc_mae_plot_umap	Man page Source code
sc_sample_data	Man page
sc_sample_qc	Man page
sc_trim_barcode	Man page Source code
validObject	Source code
validate_saf	Source code