Recent changes to GEAR

GEAR modified by Guobo Chen

Guobo Chen — Sat, 09 May 2015 11:38:35 -0000

--- v44
+++ v45
@@ -31,7 +31,7 @@
 + [Data manager](https://sourceforge.net/p/gbchen/wiki/DataManager/ "Data manager")
 + Meta-analysis
     * [Meta watchdog](https://sourceforge.net/p/gbchen/wiki/Meta-watchdog/ "Meta watchdog")
-    * [LambdaMeta](https://sourceforge.net/p/gbchen/wiki/LambdaD/ "LambdaMeta")
+    * [LambdaMeta](https://sourceforge.net/p/gbchen/wiki/LambdaMeta/ "LambdaMeta")
     * [sfst](https://sourceforge.net/p/gbchen/wiki/SFst/ "sfst")
     * [Gmeta](https://sourceforge.net/p/gbchen/wiki/GMeta/ "Generalized meta analysis")

GEAR modified by Guobo Chen

Guobo Chen — Thu, 07 May 2015 11:53:25 -0000

--- v43
+++ v44
@@ -31,7 +31,7 @@
 + [Data manager](https://sourceforge.net/p/gbchen/wiki/DataManager/ "Data manager")
 + Meta-analysis
     * [Meta watchdog](https://sourceforge.net/p/gbchen/wiki/Meta-watchdog/ "Meta watchdog")
-    * [LambdaD](https://sourceforge.net/p/gbchen/wiki/LambdaD/ "meta lambda")
+    * [LambdaMeta](https://sourceforge.net/p/gbchen/wiki/LambdaD/ "LambdaMeta")
     * [sfst](https://sourceforge.net/p/gbchen/wiki/SFst/ "sfst")
     * [Gmeta](https://sourceforge.net/p/gbchen/wiki/GMeta/ "Generalized meta analysis")

GEAR modified by Guobo Chen

Guobo Chen — Mon, 27 Apr 2015 03:42:58 -0000

--- v42
+++ v43
@@ -32,7 +32,9 @@
 + Meta-analysis
     * [Meta watchdog](https://sourceforge.net/p/gbchen/wiki/Meta-watchdog/ "Meta watchdog")
     * [LambdaD](https://sourceforge.net/p/gbchen/wiki/LambdaD/ "meta lambda")
+    * [sfst](https://sourceforge.net/p/gbchen/wiki/SFst/ "sfst")
     * [Gmeta](https://sourceforge.net/p/gbchen/wiki/GMeta/ "Generalized meta analysis")
+

 + [High Performance Computing](https://sourceforge.net/p/gbchen/wiki/High%20Performance%20Computing/ "Submit an analysis to the cluster")

GEAR modified by Guobo Chen

Guobo Chen — Sat, 27 Dec 2014 13:16:23 -0000

--- v41
+++ v42
@@ -20,6 +20,7 @@
 7. [Projected PC](https://sourceforge.net/p/gbchen/wiki/propc/ "Generating projected PC")
 8. [Profile scores](https://sourceforge.net/p/gbchen/wiki/Profiling%20score/ "Generating profile scores for GWAS data")
 9. Simulation
+    * [Polygenic for quantitative traits](https://sourceforge.net/p/gbchen/wiki/QTPolygenicSimu/ "simulating polygenic model for quantitative traits")
     * [Polygenic traits simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
     * [Discordant nuclear family simulation](https://sourceforge.net/p/gbchen/wiki/SimuFamily/ "Simulation for nuclear family")
     * [GWAS data simulation](https://sourceforge.net/p/gbchen/wiki/RealdataSimu/ "GWAS data simulation")

GEAR modified by Guobo Chen

Guobo Chen — Mon, 22 Dec 2014 03:19:00 -0000

--- v40
+++ v41
@@ -20,7 +20,7 @@
 7. [Projected PC](https://sourceforge.net/p/gbchen/wiki/propc/ "Generating projected PC")
 8. [Profile scores](https://sourceforge.net/p/gbchen/wiki/Profiling%20score/ "Generating profile scores for GWAS data")
 9. Simulation
-    * [Polygenic simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
+    * [Polygenic traits simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
     * [Discordant nuclear family simulation](https://sourceforge.net/p/gbchen/wiki/SimuFamily/ "Simulation for nuclear family")
     * [GWAS data simulation](https://sourceforge.net/p/gbchen/wiki/RealdataSimu/ "GWAS data simulation")
 + [Hong Lee's transformation for heritability](https://sourceforge.net/p/gbchen/wiki/Hong%20Lee%27s%20Transformation%20for%20Heritability/ "Transformation of the h2 between the observed scale and the liability scale")

GEAR modified by Guobo Chen

Guobo Chen — Mon, 22 Dec 2014 03:18:26 -0000

--- v39
+++ v40
@@ -22,6 +22,7 @@
 9. Simulation
     * [Polygenic simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
     * [Discordant nuclear family simulation](https://sourceforge.net/p/gbchen/wiki/SimuFamily/ "Simulation for nuclear family")
+    * [GWAS data simulation](https://sourceforge.net/p/gbchen/wiki/RealdataSimu/ "GWAS data simulation")
 + [Hong Lee's transformation for heritability](https://sourceforge.net/p/gbchen/wiki/Hong%20Lee%27s%20Transformation%20for%20Heritability/ "Transformation of the h2 between the observed scale and the liability scale")
 + [BLUP](https://sourceforge.net/p/gbchen/wiki/BLUP/ "BLUP")
 + [Quick IBD](https://sourceforge.net/p/gbchen/wiki/QuickIBD/ "IBD")

GEAR modified by Guobo Chen

Guobo Chen — Mon, 22 Dec 2014 02:30:34 -0000

--- v38
+++ v39
@@ -11,26 +11,28 @@
 The following procedures have already been included into gear.

 1. [Naive imputation](https://sourceforge.net/p/gbchen/wiki/NaiveImputation/ "naive imputation")
-+ [Generate genetic relatedness scores](https://sourceforge.net/p/gbchen/wiki/GenerateGRM/ 
+2. [Generate genetic relatedness scores](https://sourceforge.net/p/gbchen/wiki/GenerateGRM/ 
 "GRM scores")
-
-+ [Fst](https://sourceforge.net/p/gbchen/wiki/Fst/ "Fst")
-+ [Haseman-Elston regression](https://sourceforge.net/p/gbchen/wiki/Haseman-Elston%20regression%20for%20association/ "Haseman-Elston regression for GWAS")
-+ [Genetic relationship statistics (effective number of markers)](https://sourceforge.net/p/gbchen/wiki/Inference%20of%20effective%20markers/ "Inference of the effective number of markers and individuals given genetic relationship matrix")
-+ [DNA Fingerprint](https://sourceforge.net/p/gbchen/wiki/DNA%20Fingerprint/ "Pairwise comparison of genetic similarity based on SNP data")
-+ [Projected PC](https://sourceforge.net/p/gbchen/wiki/propc/ "Generating projected PC")
-+ [Profile scores](https://sourceforge.net/p/gbchen/wiki/Profiling%20score/ "Generating profile scores for GWAS data")
-+ [Polygenic simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
-+ [Discordant nuclear family simulation](https://sourceforge.net/p/gbchen/wiki/SimuFamily/ "Simulation for nuclear family")
-+ [High Performance Computing](https://sourceforge.net/p/gbchen/wiki/High%20Performance%20Computing/ "Submit an analysis to the cluster")
+3. [Fst](https://sourceforge.net/p/gbchen/wiki/Fst/ "Fst")
+4. [Haseman-Elston regression](https://sourceforge.net/p/gbchen/wiki/Haseman-Elston%20regression%20for%20association/ "Haseman-Elston regression for GWAS")
+5. [Genetic relationship statistics (effective number of markers)](https://sourceforge.net/p/gbchen/wiki/Inference%20of%20effective%20markers/ "Inference of the effective number of markers and individuals given genetic relationship matrix")
+6. [DNA Fingerprint](https://sourceforge.net/p/gbchen/wiki/DNA%20Fingerprint/ "Pairwise comparison of genetic similarity based on SNP data")
+7. [Projected PC](https://sourceforge.net/p/gbchen/wiki/propc/ "Generating projected PC")
+8. [Profile scores](https://sourceforge.net/p/gbchen/wiki/Profiling%20score/ "Generating profile scores for GWAS data")
+9. Simulation
+    * [Polygenic simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
+    * [Discordant nuclear family simulation](https://sourceforge.net/p/gbchen/wiki/SimuFamily/ "Simulation for nuclear family")
 + [Hong Lee's transformation for heritability](https://sourceforge.net/p/gbchen/wiki/Hong%20Lee%27s%20Transformation%20for%20Heritability/ "Transformation of the h2 between the observed scale and the liability scale")
 + [BLUP](https://sourceforge.net/p/gbchen/wiki/BLUP/ "BLUP")
 + [Quick IBD](https://sourceforge.net/p/gbchen/wiki/QuickIBD/ "IBD")
 + [HE linkage](https://sourceforge.net/p/gbchen/wiki/HELink/ "HE linkage")
 + [Data manager](https://sourceforge.net/p/gbchen/wiki/DataManager/ "Data manager")
-+ [Meta watchdog](https://sourceforge.net/p/gbchen/wiki/Meta-watchdog/ "Meta watchdog")
-+ [LambdaD](https://sourceforge.net/p/gbchen/wiki/LambdaD/ "meta lambda")
-+ [Gmeta](https://sourceforge.net/p/gbchen/wiki/GMeta/ "Generalized meta analysis")
++ Meta-analysis
+    * [Meta watchdog](https://sourceforge.net/p/gbchen/wiki/Meta-watchdog/ "Meta watchdog")
+    * [LambdaD](https://sourceforge.net/p/gbchen/wiki/LambdaD/ "meta lambda")
+    * [Gmeta](https://sourceforge.net/p/gbchen/wiki/GMeta/ "Generalized meta analysis")
+
++ [High Performance Computing](https://sourceforge.net/p/gbchen/wiki/High%20Performance%20Computing/ "Submit an analysis to the cluster")

 **Citation:**
 Chen G.B. (2014) Estimating heritability of complex traits from genome- wide association studies using IBS-based Haseman–Elston regression. [Front. Genet. 5:107](http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00107/abstract).

GEAR modified by Guobo Chen

Guobo Chen — Wed, 10 Dec 2014 00:27:05 -0000

--- v37
+++ v38
@@ -18,6 +18,7 @@
 + [Haseman-Elston regression](https://sourceforge.net/p/gbchen/wiki/Haseman-Elston%20regression%20for%20association/ "Haseman-Elston regression for GWAS")
 + [Genetic relationship statistics (effective number of markers)](https://sourceforge.net/p/gbchen/wiki/Inference%20of%20effective%20markers/ "Inference of the effective number of markers and individuals given genetic relationship matrix")
 + [DNA Fingerprint](https://sourceforge.net/p/gbchen/wiki/DNA%20Fingerprint/ "Pairwise comparison of genetic similarity based on SNP data")
++ [Projected PC](https://sourceforge.net/p/gbchen/wiki/propc/ "Generating projected PC")
 + [Profile scores](https://sourceforge.net/p/gbchen/wiki/Profiling%20score/ "Generating profile scores for GWAS data")
 + [Polygenic simulation](https://sourceforge.net/p/gbchen/wiki/Simulation%20for%20polygenic%20models/ "Simulate genetic data and phenotypes for polygenic models")
 + [Discordant nuclear family simulation](https://sourceforge.net/p/gbchen/wiki/SimuFamily/ "Simulation for nuclear family")

GEAR modified by Guobo Chen

Guobo Chen — Wed, 05 Nov 2014 07:16:33 -0000

--- v36
+++ v37
@@ -1,10 +1,9 @@
 __GEAR: GEnetic Analysis Repository__
 Contributed by **geneticker**: a geneticist and a hacker
 * * *
+[[download_button]]

 ![External](https://sourceforge.net/p/gbchen/wiki/GEAR/attachment/Sibila_Libica.jpg)
-
-[[download_button]]

 The general option to call gear is "java -jar gear.jar".
 It is easy to define alias on your own computer in which you define "alias gear=java -jar  **/path/**gear.jar ".  **/path/** is the location of gear.jar on your computer.

GEAR modified by Guobo Chen

Guobo Chen — Wed, 05 Nov 2014 07:16:01 -0000

--- v35
+++ v36
@@ -4,6 +4,7 @@

 ![External](https://sourceforge.net/p/gbchen/wiki/GEAR/attachment/Sibila_Libica.jpg)

+[[download_button]]

 The general option to call gear is "java -jar gear.jar".
 It is easy to define alias on your own computer in which you define "alias gear=java -jar  **/path/**gear.jar ".  **/path/** is the location of gear.jar on your computer.