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1. Introduction
2. Basic information
3. Download and general notes
4. Command reference table
5. Basic usage/data formats
6. Data management
7. Summary stats
8. Inclusion thresholds
9. Population stratification
10. IBS/IBD estimation
11. Association
12. Family-based association
13. Permutation procedures
14. LD calculations
15. Multimarker tests
16. Conditional haplotype tests
17. Proxy association
18. Imputation (beta)
19. Dosage data
20. Meta-analysis
21. Annotation
22. LD-based results clumping
23. Gene-based report
24. Epistasis
25. Rare CNVs
26. Common CNPs
27. R-plugins
28. Annotation web-lookup
29. Simulation tools
30. Profile scoring
31. ID helper
32. Resources
33. Flow-chart
34. Miscellaneous
35. FAQ & Hints
36. gPLINK
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Credits
PLINK is developed by Shaun Purcell, with the help of
others.
In particular, Douglas Ruderfer has contributed to many internal
functions and has performed extensive testing.
Below is a list of others who have been involved in
one way or another:
- Paul de Bakker: testing and many detailed suggestions
- David Bender: Haploview interface for veiwing PLINK results
- Mark Daly: various statistical and computational algorithms
- Julian Maller: Haploview interface for veiwing PLINK results
- Ben Neale: IBD estimation routines
- Robert Plenge: early beta-testing
- Lori Thomas: development of PLINK-O-MATIC and beta version of gPLINK
- Kathe Todd-Brown: gPLINK development
- Pak Sham: IBD estimation and other association routines
and others at MGH, the Broad Institute and elsewhere. Thanks!
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