Man pages for LiuzLab/TraceQC
Quality Control of CRISPR Lineage Tracing Seqence Data
| build_binary_table | Convert A TraceQC object to a matrix |
| create_obj_list | Create a list of TraceQC objects from a list |
| create_TraceQC_object | Creating an input object for TraceQC with an alignment... |
| example_obj | An example TraceQC object |
| example_obj_list | An example of a list of TraceQC objects |
| fastqc.file | Running FASTQC for a file. |
| generate_qc_report | Create a HTML QC report |
| generate_qc_report_from_obj | Create a HTML QC report from TraceQC object |
| get_qcpath | Function to locate where the Quality Control file is stored. |
| install_external_packages | Installation necessary external software for TraceQC |
| mutation_type | A pie chart that shows a summary of mutation types. |
| plot_mutation_pattern_lineplot | Plot the mutation pattern of given samples using a line plot. |
| plot_mutation_pattern_violinplot | Plot the mutation pattern of given samples using a violin... |
| plot_phylogenetic_tree | Plot a phylogenetic tree of a tree object using ggtree |
| plot_point_mutation_hotspot | Display a mutation hotspot circos plot. |
| sequnce_alignment_threshold | Function for finding threshold of sequence alignment. The... |
| table_to_phyDat | Convert a binary table of mutation events to a phyDat object |
| TraceQC | Creating an input object for TraceQC |
