qgene.org

QGene

We will post here news about QGene updates. Current version is: 4.3.10. Key to release numbering. The first number (here, 4. Describes the base feature package. If we add features, we kick up the second number: 4.4. If we fix bugs in 4.4. We tack on a third number: 4.4.1. This lets us fix unlimited bugs in 4.4. Without reaching 4.5. If we add important functionality we're ready to move up to version 5.0. As your double-clickable launcher (for most convenience, add it to your Startup menu as a shortcut).

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QGene | qgene.org Reviews

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We will post here news about QGene updates. Current version is: 4.3.10. Key to release numbering. The first number (here, 4. Describes the base feature package. If we add features, we kick up the second number: 4.4. If we fix bugs in 4.4. We tack on a third number: 4.4.1. This lets us fix unlimited bugs in 4.4. Without reaching 4.5. If we add important functionality we're ready to move up to version 5.0. As your double-clickable launcher (for most convenience, add it to your Startup menu as a shortcut).

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QGene | qgene.org Reviews

https://qgene.org

We will post here news about QGene updates. Current version is: 4.3.10. Key to release numbering. The first number (here, 4. Describes the base feature package. If we add features, we kick up the second number: 4.4. If we fix bugs in 4.4. We tack on a third number: 4.4.1. This lets us fix unlimited bugs in 4.4. Without reaching 4.5. If we add important functionality we're ready to move up to version 5.0. As your double-clickable launcher (for most convenience, add it to your Startup menu as a shortcut).

INTERNAL PAGES

qgene.org

1

QTL analysis

http://www.qgene.org/qgene/current/docs/manual/QTL_analysis.html

This is the window where most of your QGene work will be done. It looks like this. Selection of chromosomes and traits in their respective lists at left is according to standard rules; a mouse click selects one at a time unless you hold down the Control key (for possibly non-adjacent selections) or the Shift key (for extending a selection). Double-clicking on a trait name allows you to change the color used for its contours. These analyses are discussed in more statistical detail on a separate page.

2

eQTL analysis

http://www.qgene.org/qgene/current/docs/manual/eQTL_analysis.html

Expression data can be subjected to the same QTL analyses as ordinary trait data. For this the main QTL-mapping window may be used. Usually, however, analysts will want to view a "heat map" showing the combined results from all of the e-traits. Further operations may include network reconstruction and export, not yet available as of QGene version 4.3. Page explains the modified format necessary for including physical positions for e-traits and markers in an eQTL data set. Once your eQTL .qdf. If the firs...

3

QGene data format

http://www.qgene.org/qgene/current/docs/manual/Data_format.html

The standard format for importing marker, map, and trait data into QGene is as a .qdf. File, which is structured as follows:. Starting with version 4.3, which allows eQTL analysis, the .qdf. Format can also accommodate e-trait data and the markers used for an eQTL experiment. In this case one line of the header must consist of the word eQTL. Explanation of .qdf format. The three content keywords in square brackets tell QGene the content of the material following them, up to the next keyword. The dominant...

4

QTL analysis plugins

http://www.qgene.org/qgene/current/docs/manual/QTL_analysis_plugins.html

All QGene's QTL, marker, and trait-analysis methods are written as plugins. A plugin is a relatively small piece of program code meant to be "plugged in" to a larger program that finds it after the larger program is started by the user. If you are a developer, you already know this. If you aren't, it's all you need to know. The purpose of this page is to describe each of the plugin analyses we've provided. Others will be described as they are contributed. Plugins for the QTL analysis window. Additive eff...

5

QGene

http://www.qgene.org/qgene/old-news.php

This is an archive of QGene updates. If you have trouble launching QGene in Windows, first try moving the QGene folder off your desktop onto your C drive. Why? If your name contains non-English characters such as ä and you install QGene on your desktop, the file path to QGene will have your name in it, and Java refuses to follow such paths. This is not our fault - it's a Java problem. If you have trouble launching QGene in Windows,. Please replace the launcher with this one. Files in the zip file,. We im...

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We will post here news about QGene updates. Current version is: 4.3.10. Key to release numbering. The first number (here, 4. Describes the base feature package. If we add features, we kick up the second number: 4.4. If we fix bugs in 4.4. We tack on a third number: 4.4.1. This lets us fix unlimited bugs in 4.4. Without reaching 4.5. If we add important functionality we're ready to move up to version 5.0. As your double-clickable launcher (for most convenience, add it to your Startup menu as a shortcut).

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