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= [wiki:xQTL xQTL workbench] - Manual =

New biotechnologies enable exciting QTL experiments that link genetic variation to 'all' gene expression, protein and metabolite traits.
Powerful software and hardware are available to analyze these new data but the considerable effort needed to configure pipelines, to scale
up processing and to track raw, intermediate and result data are a barrier for most except a small community of experts. Here we report
XGAP/cluster: a collaborative effort to bring seamless data management, advanced analytical pipelines and high throughput cluster computing
together in one box to biologists workbench. xQTL workbench is created from the modular [wiki:MolgenisApps/Architecture molgenis_apps] software suite.

[http://molgenis02.target.rug.nl:8080/xqtl Try the online xQTL workbench demo][[BR]]
[http://molgenis02.target.rug.nl/download/xqtl_workbench.zip Download xQTL workbench] (unzip, '''run.bat''' or '''run.sh''' to start, or check [wiki:xQTLAdministratorDownload Download instructions] for details)[[BR]]
 * [wiki:xQTL Table of Contents]
   * [wiki:xQTLIntroduction Introduction]
   * '''Biologist'''
     * [wiki:xQTLBiologistLogin Registration and login]
     * [wiki:xQTLBiologistBrowse Browse or search available data]
     * [wiki:xQTLBiologistImport Import new data]
     * [wiki:xQTLBiologistRun Run QTL mapping]
   * '''Bioinformatician'''
     * [wiki:xQTLBioinformaticianScript Add a new R script]
     * [wiki:xQTLBioinformaticianTag Tag data and configure parameters]
     * [wiki:xQTLBioinformaticianAnalysis Setup a new runnable analysis]
     * [wiki:xQTLBioinformaticianGalaxy Galaxy and Cloud]
     * [wiki:xQTLBioinformaticianRCheatSheet Cheat sheet for R scripting]
   * '''Administrator'''
     * [wiki:xQTLAdministratorDownload Installation instructions]
     * [wiki:xQTLAdministratorPermissions Manage users and permissions]
     * [wiki:xQTLAdministratorDatabase Manage database and storage]
     * [wiki:xQTLAdministratorInstall Server/development installation]
     * [wiki:xQTLAdministratorJobs Setup job submission]
   * '''Tutorial'''
     * [wiki:xQTLTutorialStart Overview of the tutorial]
     * [wiki:xQTLTutorialBiologistUploadingData Uploading a new dataset]
     * [wiki:xQTLTutorialBiologistInspectingData Inspecting the uploaded data]
     * [wiki:xQTLTutorialBiologistRunningAnalysis Running a basic QTL analysis]
     * [wiki:xQTLTutorialBiologistBrowsingResults Browse and interpret results]