Introduction | Data Preparation | Create mock GTF and Test Sets | Initial Filtering and Feature Extraction | Coding Potential Analysis | Aggregation and Venn Visualization | Performance Evaluation | Performance Visualization with calculateCM | Radar and Clock Plots | Functional Analysis and Interactions | Cis and Trans Interactions | Annotation and Sankey Diagram | Session Information

1 Introduction | 1.1 Instalation and loading | 2 Data manipulation and overall usage | 2.1 GUI | 2.2 Command Line | 2.2.1 List of functions and their description | runPsScan() | readPsa() and readProsite() | gff2matrix() | matrix2hm() and matrixToSquareHeatmap() | extractSegments() and extractProteinMotifs() | extractProteinMotifs() | freqPie() | References | Session Information