Pipeline for single cell multi-omic data pre-processing


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Documentation for package ‘scPipe’ version 2.8.0

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scPipe-package scPipe - single cell RNA-seq pipeline
.qq_outliers_robust Detect outliers based on robust linear regression of QQ plot
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
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
feature_info Get or set 'feature_info' from a SingleCellExperiment object
feature_info-method Get or set 'feature_info' from a SingleCellExperiment object
feature_info.sce Get or set 'feature_info' from a SingleCellExperiment object
feature_info<- Get or set 'feature_info' from a SingleCellExperiment object
feature_info<--method Get or set 'feature_info' from a SingleCellExperiment object
feature_type Get or set 'feature_type' from a SingleCellExperiment object
feature_type-method Get or set 'feature_type' from a SingleCellExperiment object
feature_type.sce Get or set 'feature_type' from a SingleCellExperiment object
feature_type<- Get or set 'feature_type' from a SingleCellExperiment object
feature_type<--method Get or set 'feature_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
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_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 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
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
TF.IDF.custom Returns the TF-IDF normalised version of a binary matrix
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