5 Scripting and Other Integrated Statistical Tools

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 5.1 Integrated Tools Overview
 5.2 The Python Shell Window
  5.2.1 Using Shell Objects
  5.2.2 Using the Dir Command
  5.2.3 Using Python for Getting Help
 5.3 Running Scripts
  5.3.1 Command Line Invocation
  5.3.2 Python Shell Invocation
  5.3.3 Navigator Menu Invocation
  5.3.4 Script Server Invocation
 5.4 Selecting a Script Server
 5.5 Example Scripts
 5.6 Scripting Reference
  5.6.1 Project Related Commands
  5.6.2 General GHI Commands
  5.6.3 Commands Common to All Objects
  5.6.4 Importing and Loading Data
  5.6.5 Creating a New Data Set with Scripting
  5.6.6 Spreadsheet Access and Manipulation
  5.6.7 Using the Linkage Disequilibrium Object
  5.6.8 Using the Hardy Weinberg Object
  5.6.9 Using the Two-Loci Object
  5.6.10 Using the P-Value plot
  5.6.11 Getting and Setting Tree Options
  5.6.12 Creating a Tree Model
  5.6.13 Importing a Legacy Tree Model
  5.6.14 Tree Model Commands
  5.6.15 Using the Distance Matrix Object
  5.6.16 Applying a Tree Model
  5.6.17 Copy Number Analysis
  5.6.18 Importing Raw Copy Number Values
  5.6.19 Performing LogR Association Tests and PCA
  5.6.20 Performing Regression
  5.6.21 Output a C File
  5.6.22 Prompting the User for Input
  5.6.23 Text Viewer
  5.6.24 Regression Results
  5.6.25 Navigator Object Selection
 5.7 S-PLUS Integration
  5.7.1 S-PLUS Desktop Integration
  5.7.2 S-PLUS Client/Server Integration
 5.8 R Integration
 5.9 PBAT Integration

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