# pipeline for single cell RNA-seq data analysis

## Documentation for package ‘scPipe’ version 1.16.0

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

## Help Pages

scPipe-package | scPipe - single cell RNA-seq pipeline
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
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
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_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
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
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