# Cellular DNA Barcode Analysis toolkit

## Documentation for package ‘CellBarcode’ version 1.16.0

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

## Help Pages

CellBarcode-package | DNA Barcode Analysis toolkit
*.BarcodeObj | Manages barcodes and samples in a BarcodeObj object
+.BarcodeObj | Manages barcodes and samples in a BarcodeObj object
-.BarcodeObj | Manages barcodes and samples in a BarcodeObj object
BarcodeObj | BarcodeObj object
BarcodeObj-class | BarcodeObj object
BarcodeQc | Evaluates sequences quality
BarcodeQc-class | Evaluates sequences quality
BarcodeQcSet | Evaluates sequences quality
BarcodeQcSet-class | Evaluates sequences quality
bc_2df | Transforms BarcodeObj object into another data type
bc_2df-method | Transforms BarcodeObj object into another data type
bc_2dt | Transforms BarcodeObj object into another data type
bc_2dt-method | Transforms BarcodeObj object into another data type
bc_2matrix | Transforms BarcodeObj object into another data type
bc_2matrix-method | Transforms BarcodeObj object into another data type
bc_auto_cutoff | Finds barcode count cutoff point
bc_auto_cutoff-method | Finds barcode count cutoff point
bc_barcodes | Gets barcode sequences
bc_barcodes-method | Gets barcode sequences
bc_cleanBc | Accesses cleanBc slot in the BarcodeObj object
bc_cleanBc-method | Accesses cleanBc slot in the BarcodeObj object
bc_create_BarcodeObj | Create a BarcodeObj object from extracted barcodes data
bc_create_BarcodeObj-method | Create a BarcodeObj object from extracted barcodes data
bc_cure_cluster | Clean barcodes by editing distance
bc_cure_cluster-method | Clean barcodes by editing distance
bc_cure_depth | Filters barcodes by counts
bc_cure_depth-method | Filters barcodes by counts
bc_cure_umi | Filters UMI-barcode tag by counts
bc_cure_umi-method | Filters UMI-barcode tag by counts
bc_extract | Extract barcode from sequences
bc_extract-method | Extract barcode from sequences
bc_extract_sc_bam | Extract barcode from single-cell sequencing sam file
bc_extract_sc_fastq | Extract barcode from single-cell sequencing fastq file
bc_extract_sc_sam | Extract barcode from single-cell sequencing sam file
bc_merge | Manages barcodes and samples in a BarcodeObj object
bc_merge-method | Manages barcodes and samples in a BarcodeObj object
bc_messyBc | Accesses messyBc slot in the BarcodeObj object
bc_messyBc-method | Accesses messyBc slot in the BarcodeObj object
bc_meta | Accesses and sets metadata in BarcodeObj object
bc_meta-method | Accesses and sets metadata in BarcodeObj object
bc_meta<- | Accesses and sets metadata in BarcodeObj object
bc_meta<--method | Accesses and sets metadata in BarcodeObj object
bc_names | Access & update sample names in BarcodeObj & and BarcodeQcSet
bc_names-method | Access & update sample names in BarcodeObj & and BarcodeQcSet
bc_names<- | Access & update sample names in BarcodeObj & and BarcodeQcSet
bc_names<--method | Access & update sample names in BarcodeObj & and BarcodeQcSet
bc_obj | A dummy BarcodeObj object
bc_plot_count | Plot for counts distribution
bc_plot_count-method | Plot for counts distribution
bc_plot_mutual | Barcode read count 2D scatter plot of sample combination
bc_plot_mutual-method | Barcode read count 2D scatter plot of sample combination
bc_plot_pair | Barcode read count 2D scatter plot for given pairs
bc_plot_pair-method | Barcode read count 2D scatter plot for given pairs
bc_plot_seqQc | Evaluates sequences quality
bc_plot_seqQc-method | Evaluates sequences quality
bc_plot_single | Scatter plot of barcode count distribution per sample
bc_plot_single-method | Scatter plot of barcode count distribution per sample
bc_seq_filter | Remove low-quality sequence
bc_seq_filter-method | Remove low-quality sequence
bc_seq_qc | Evaluates sequences quality
bc_seq_qc-method | Evaluates sequences quality
bc_splitVDJ | Parse VDJ recombination (experimental)
bc_subset | Manages barcodes and samples in a BarcodeObj object
bc_subset-method | Manages barcodes and samples in a BarcodeObj object
bc_summary_barcode | Summary and evaluate barcode diversity
bc_summary_barcode-method | Summary and evaluate barcode diversity
bc_summary_seqQc | Summary barcodeQcSet
bc_summary_seqQc-method | Summary barcodeQcSet
CellBarcode | DNA Barcode Analysis toolkit
format-method | Formats BarcodeObj object
parse_10x_sam | Parse 10X bam file
seq_correct | Sequence clustering
show-method | Show BarcodeObj object
subset-method | Subset the BarcodeQcSet
[-method | Subset the BarcodeQcSet