RAREMETAL Documentation - Revision history

Abought: Update contact address

2019-05-20T17:22:15Z

Update contact address

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	==CONTACT==		==CONTACT==

	Please email ~~Sai Chen~~ (~~saichen~~ at umich dot edu) for questions.		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

2019-03-14T16:53:22Z

Download and Installation

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	== Download and Installation ==		== Download and Installation ==
	* University of Michigan CSG users can go to the following:
	~~/net/wonderland/home/saichen/Raremetal/bin/~~

	~~=== Where to Download ===~~		We have tested compilation using our source code on several platforms including Linux, and Mac OS X.

	We have tested compilation using our source code on several platforms including Linux, ~~MAC~~ OS X~~, and Windows~~.

	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''']].

2018-03-15T21:03:18Z

2017-11-15T18:02:33Z

Point Github link at statgen repo

← Older revision		Revision as of 14:02, 15 November 2017
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	== Useful Wiki Pages ==		== Useful Wiki Pages ==

	* Git hub page: https://github.com/~~traxexx~~/Raremetal		* Git hub page: https://github.com/statgen/Raremetal

	* The [[RAREMETAL_Change_Log \| Change Log]]		* The [[RAREMETAL_Change_Log \| Change Log]]

2016-11-27T19:13:29Z

Useful Wiki Pages

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	* The [[Tutorial:_RAREMETAL\|RAREMETAL Quick Start Tutorial]]		* The [[Tutorial:_RAREMETAL\|RAREMETAL Quick Start Tutorial]]
			* The [[RAREMETAL METHOD]]

	* The [[RAREMETAL FAQ]]		* The [[RAREMETAL FAQ]]

2016-07-17T16:05:41Z

Download and Installation

← Older revision		Revision as of 12:05, 17 July 2016
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	== Download and Installation ==		== Download and Installation ==
	* University of Michigan CSG users can go to the following:		* University of Michigan CSG users can go to the following:
	/net/wonderland/home/saichen/Raremetal/		/net/wonderland/home/saichen/Raremetal/bin/

	=== Where to Download ===		=== Where to Download ===

2016-07-14T17:22:22Z

Useful Wiki Pages

← Older revision		Revision as of 13:22, 14 July 2016
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	== Useful Wiki Pages ==		== Useful Wiki Pages ==

	* ~~Raremetal git~~ hub: https://github.com/traxexx/Raremetal		* Git hub page: https://github.com/traxexx/Raremetal

	* The [[RAREMETAL_Change_Log \| Change Log]]		* The [[RAREMETAL_Change_Log \| Change Log]]

2016-07-14T17:22:06Z

Useful Wiki Pages

← Older revision		Revision as of 13:22, 14 July 2016
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	== Useful Wiki Pages ==		== Useful Wiki Pages ==

			* Raremetal git hub: https://github.com/traxexx/Raremetal

	* The [[RAREMETAL_Change_Log \| Change Log]]		* The [[RAREMETAL_Change_Log \| Change Log]]

2016-07-14T17:19:01Z

Brief Description

← Older revision		Revision as of 13:19, 14 July 2016
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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.

	~~== Brief Description ==~~

	'''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.

	~~'''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 ==

2016-07-14T17:18:53Z

Key Features

← Older revision		Revision as of 13:18, 14 July 2016
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	The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] tool for rare-variant association analysis can also generate output compatible with RAREMETAL.		The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] tool for rare-variant association analysis can also generate output compatible with RAREMETAL.

			== Brief Description ==

			'''RAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. It 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. It generates high quality plots by default and has options that allow users to build reports at different levels.

			'''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''']].

	== Key Features ==		== Key Features ==