Cellular DNA Barcode Analysis toolkit
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Documentation for package ‘CellBarcode’ version 1.13.2
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 SAM file |
| seq_correct | Sequence clustering using Levenshtein or Hamming distance |
| show-method | Show BarcodeObj object |
| subset-method | Subset the BarcodeQcSet |
| [-method | Subset the BarcodeQcSet |