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SNP & Variation Suite v8.9.1 Manual
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SNP & Variation Suite

  • 1. Installing and Initializing
  • 2. Operating Instructions
    • 2.1. Understanding the Interface and Workflow
    • 2.2. Frequently Asked Questions
    • 2.3. Importing Your Data Into A Project
    • 2.4. Genetic Marker Maps and Affymetrix Library Files
    • 2.5. Spreadsheets
    • 2.6. Editing a Spreadsheet
    • 2.7. Working with Multiple Spreadsheets
    • 2.8. Genotype Data Quality Assessment and Utilities
    • 2.9. Principal Component Analysis
    • 2.10. Genotype Association Tests
    • 2.11. Genotypic Regression Analysis
    • 2.12. Meta-Analysis
    • 2.13. Methods for Mixed Linear Model Analysis
      • 2.13.1. Overview of Mixed Linear Models
      • 2.13.2. Large Kinship Matrices or Large Numbers of Samples
      • 2.13.3. Mixed Linear Model Analysis
      • 2.13.4. Mixed Linear Model Analysis with Interactions
      • 2.13.5. Genomic Best Linear Unbiased Predictors Analysis
      • 2.13.6. Genomic Best Linear Unbiased Predictors Analysis Using Bins
      • 2.13.7. Genetic Correlation of Two Traits using GBLUP
      • 2.13.8. Bayes C and C-pi Genomic Prediction Analysis
      • 2.13.9. K-Fold Cross Validation
      • 2.13.10. Predict Phenotypes From Existing Results
    • 2.14. Haplotype Association Tests and Block Detection
    • 2.15. Haplotype Trend Regression
    • 2.16. LD Reports
    • 2.17. Genotype Imputation
    • 2.18. Runs of Homozygosity Analysis
    • 2.19. PBAT Family-Based Analysis
    • 2.20. Numeric Data Quality Assessment
    • 2.21. Numeric Association Tests
    • 2.22. Numeric Regression Analysis
    • 2.23. CNAM Copy Number Analysis on Micro-Array Probe Intensities
    • 2.24. CNV Caller on Whole Genomes
    • 2.25. CNV Caller on NGS Target Regions
    • 2.26. DNA Sequence Analysis
    • 2.27. Collapsing Methods for DNA-Sequence Analysis
    • 2.28. RNA Sequencing Analysis
    • 2.29. The Result Viewer
    • 2.30. Visualizing Data
    • 2.31. GenomeBrowse: The Genomic Scale Data Visualization Tool
    • 2.32. Genome Assemblies
    • 2.33. The Data Source Library
    • 2.34. Annotation Convert Wizard
    • 2.35. Expression Editor
    • 2.36. CADD
    • 2.37. OMIM
    • 2.38. Custom Plotting Interface and Specialized Plots
    • 2.39. Scripting and Other Integrated Statistical Tools
    • 2.40. Python Application Programming Interface (API)
    • 2.41. gautil Documentation
    • 2.42. Appendix
  • 3. Formulas and Theories
    • 3.1. General Statistics
    • 3.2. Permutation Testing Methodology
    • 3.3. Linear Regression
    • 3.4. Logistic Regression
    • 3.5. Haplotype Frequency Estimation Methods
    • 3.6. Formulas for Computing Linkage Disequilibrium (LD)
    • 3.7. Formulas for Principal Component Analysis
    • 3.8. Runs Of Homozygosity (ROH) Algorithm
    • 3.9. Quantile Normalization of Affymetrix CEL Files
    • 3.10. CNAM Optimal Segmentation Algorithm
  • 4. EULA
  • 5. A Glossary of Terms Used in Genetic Analysis
  • 6. References

References

  • WebSite for SVS
  • Golden Helix Blog
  • Tutorials & Resources
  • Release Notes
  • Add-On Scripts

SNP & Variation Suite Manual¶

Version 8.9.1 (Previous versions)

Copyright © 2000-2021 Golden Helix, Inc.

Trademarks Used

Golden Helix SVS is a registered trademark of Golden Helix.

SNP & Variation Suite

  • 1. Installing and Initializing
  • 2. Operating Instructions
  • 3. Formulas and Theories
  • 4. EULA
  • 5. A Glossary of Terms Used in Genetic Analysis
  • 6. References

References

  • WebSite for SVS
  • Golden Helix Blog
  • Tutorials & Resources
  • Release Notes
  • Add-On Scripts
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1. Installing and Initializing
Copyright © 2021, Golden Helix