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RAREMETAL Documentation (view source)

Revision as of 13:22, 20 May 2019

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[[Category:RAREMETAL]]
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== Useful Wiki Pages ==
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== Useful Wiki Pages ==
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* Git hub page: https://github.com/statgen/Raremetal
    
* The [[RAREMETAL_Change_Log | Change Log]]
 
* The [[RAREMETAL_Change_Log | Change Log]]
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* The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]]
 
* The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]]
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* The [[RAREMETAL METHOD]]
    
* The [[RAREMETAL FAQ]]
 
* The [[RAREMETAL FAQ]]
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* Allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.
 
* Allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.
 
* Generate QQ plots and manhattan plots by default.
 
* Generate QQ plots and manhattan plots by default.
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== Brief Description ==
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'''RAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''RAREMETAL''' takes summary statistics and LD matrices generated by [[Rare-Metal-Worker|'''RAREMETALWORKER''']] or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''RAREMETAL''' generates high quality plots by default and has options that allow users to build reports at different levels.
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'''RAREMETAL''' is developed by Shuang Feng, Dajiang Liu and Gonçalo Abecasis. A R-package written by Dajiang Liu using the same methodology is [[RareMetals|'''available''']].
      
== Approach ==
 
== Approach ==
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== Download and Installation ==
 
== Download and Installation ==
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* University of Michigan CSG users can go to the following:
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  /net/wonderland/home/saichen/Raremetal/
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=== Where to Download ===
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We have tested compilation using our source code on several platforms including Linux, MAC OS X, and Windows.  
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We have tested compilation using our source code on several platforms including Linux, and Mac OS X.  
    
For source code and executables together with instructions of building from source, please go to [[RAREMETAL_DOWNLOAD_%26_BUILD |'''DOWNLOAD source and executables''']].
 
For source code and executables together with instructions of building from source, please go to [[RAREMETAL_DOWNLOAD_%26_BUILD |'''DOWNLOAD source and executables''']].
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==CONTACT==
 
==CONTACT==
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Please email Sai Chen (saichen at umich dot edu) for questions.
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Please email Andy Boughton (abought at umich dot edu) for questions.
    
Also check  [[Raremetal Incoming updates | '''Known issues and incoming update in next version''']] to see if your problem has been reported before
 
Also check  [[Raremetal Incoming updates | '''Known issues and incoming update in next version''']] to see if your problem has been reported before
Abought
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