Introduction | Figure 1: Multi-sample Analysis | 1B. CCF Heatmap | 1C. CCF Summary Heatmap | 1D. Clone Genome Distribution Plot | 1G. Multi-sample Phylogenetic Tree | 1G. Single-sample Phylogenetic Tree | Figure 2: Phylogenetic tree features | 2A. Sample-specific subclones | 2B. Annotated single-sample phylogenetic tree | 2C. Mutation timeline tree | 2D. Radial mode with 2 edges | 2E. Dendrogram mode with 2 edges | 2F. Mixed mode with 2 edges | 2G. 500 node phylogentic tree

Introduction | Methodology | Overview | Simulating null data | Parallelization in OutSeekR | Output | Example

Introduction | Input data | Input importation | Importing VCF data | Imported VCF data structures | Importing polygenic score data | Importing phenotype data | Creating a BED-formatted coordinate file | Conversion of PGS weight files to a coordinate file in BED format | Merging coordinates from multiple polygenic scores | Input data validation | Polygenic Score Application | Basic usage | combine.vcf.with.pgs | Allele matching | Missing genotype methods | Custom percentiles | Phenotype analysis | Data Visualization | Common plotting arguments | PGS Density | Basic plot | Add phenotypes | PGS Boxplot | PGS Correlation | PGS Percentile Rank | Optional arguments | Case-control analysis | Basic Plot | Binarize Continuous Phenotypes

Introduction to bedr package | Author(s): Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Paul C. Boutros | Dated: r Sys.Date() | Table of Contents | Introduction | Third Party Tools | General Region Utilities | Load bedr Library | Validate Region | Sort Region | Merge Regions | Subtract Region | in Region | Intersect/Join Regions | Statistically Quantify Regions' Similarity (jaccard and reldist) | GroupBy | Example Workflow 1: Compare Variant Callers | Example Workflow 2: Exome Target Processing | Example Workflow 3: Copy Number Recurrence | Summary | Acknowledgements

Introduction | Installation | CRAN (recommended) | GitHub | Basic Phylogenetic Tree Visualization | Input Phylogenetic Data | Simple Example | Ex. 1.1: Minimal Tree | Ex. 1.2: Using node.id, parent and label columns | Ex. 1.3: Branch Lengths | Ex. 1.4: Branch Scaling | Ex. 1.5: Y-Axis Labels | Ex. 1.6: Axis Tick Placement | Ex. 1.7: Scale Bars | Ex. 1.8: Visualizing Cellular Prevalence | Customizing Node Arrangement | Ex. 2.1: Node Spread | Ex. 2.2: Node Angles | Phylogenetic Tree Modes | Ex. 3.1: Radial Mode | Ex. 3.2: Dendrogram Mode | Customizing Phylogenetic Tree Aesthetics | Supported Aesthetic Input Columns | Line Types | Ex. 4.1: Styled Tree | Ex. 4.2: Nodeless Tree | Text Annotations | Ex. 5.1: Edge annotations | Ex. 5.2: Specifying Text Colour and Style | Additional Plot Parameters | Ex. 6.1: Adding the Normal Node | Ex. 6.2: Horizontal Padding Between Tree and Axes | Ex. 6.3: Plot Title | Ex. 6.4: Saving Plot to file | CCF Distribution Visualization | Input SNV-to-subclone Assignment Data | Ex. 7.1: CCF Distribution Heatmap | Ex. 7.2: CCF Distribution Across subclones | Ex. 7.3: Summary of CCF Distribution | Ex. 7.4: Clone-Genome Distribution Plot

Introduction | Setup | Generation and aggregation of z-scores | Calculation of z-scores | Adjusting metric directionality | Calculating total quality score | Outlier detection using cosine similarity | Finding the best fitting distribution | The iterative method for outlier nomination using cosine similarity | The cutoff method for outlier nomination using cosine similarity | Data visualisation | Quality score barplot | Z-score heatmap | Aggregating the plots

Background | Approach | Input | Running SeqKat | Output | Example | References