Chapter 3. Reference
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Chapter 3. Reference
Table of Contents
3.1. Running Caryoscope
3.1.1. Running from the Web
3.1.2. Running from a local installation
3.1.2.1. Running from a graphical interface
3.1.2.2. Running from the command line
3.2. Settings
3.2.1. General concepts
3.2.2. Axis line color
3.2.3. Axis line thickness
3.2.4. Centromere shown
3.2.5. Chromosome axis shown
3.2.6. Data scale increment
3.2.7. Data scale shown
3.2.8. Feature tooltip expression
3.2.9. Feature URL expression
3.2.10. Logarithm base
3.2.11. Lograrithm enabled
3.2.12. Minimum feature width
3.2.13. Moving average enabled
3.2.14. Moving average half decay distance
3.2.15. Moving average half window width
3.2.16. Negative value color
3.2.17. Positive value color
3.2.18. Scale line color
3.2.19. Scale line thickness
3.2.20. View background color
3.3. Viewing your data
3.3.1. Reset Viewpoint
3.3.2. Dynamic Zoom mode
3.3.3. Dynamic Pan mode
3.3.4. Zoom In mode
3.3.5. Zoom Out mode
3.3.6. Navigate Mode
3.3.7. Scroll bars
3.4. Input file formats
3.4.1. General Feature Format
3.4.1.1. Chromosome definition
3.4.1.2. Centromere definition
3.4.1.3. Feature definition
3.4.2. Spreadsheet-compatible text
3.5. Transforming your data
3.5.1. Built-in transformations
3.5.1.1. Logarithm calculation
3.5.1.2. Moving average calculation
3.5.2. External calculations
3.6. Other concepts
3.6.1. Expressions using annotations
3.6.2. Specifying colors in hexadecimal format
3.7. Integrating with the Stanford Microarray Database