Array Viewer Links

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Warning.png WARNING: Array Viewer and is no longer supported for OmicSoft Suite v12 and above.


Contents

Overview

Content on Array Server can be shared easily by creating links to the content and sending links to colleagues. Other users on the Array Server can open the link to instantly view the content on the server without searching or browsing. The link will open an Array Viewer instance, which display all the contents shared in the link, but the users cannot modify the content in Array Viewer.

Tips.png Links to editable projects can be created with Open Array Studio Launcher


Creating Array Viewer Links

Array Viewer links can be created in the Server tab from the Viewer Wizard, by selecting Share a non-editable version of the project...

ProjectAction Window ArrayViewer.png

General Server Link

Use of "server = server url" in the link can open an Array Viewer instance connecting to the server specified.

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer

Server Project

Open Server Project by ID

Use of "projectid = Project ID" in the link can open the specified project in Array Server.

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&projectid=gse30004

Open An Existing Project Collection/List

projectlist = project list ID

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&projectlist=916d95d7f20c6eb4

Open One Single Gene in a Server Project

id=masterid|egr1

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&projectid=gse30004&id=masterid%7Cegr1


or just (the above example can use rowid for probeset ids): id=egr1

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&projectid=gse30004&id=egr1

Open Multiple Genes in a Server Project

id=egr1,egr2

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&projectid=gse30004&id=egr1,egr2

Genome Browser

Open a shared genome browser with id: gb000018

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&browserid=gb000018

Open a shared genome browser with id: gb000018 and jump to region: 7:55086725-55275031

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&browserid=gb000030&region=7:55086725-55275031

Land

Open Land by Land Name

This opens the summary statistics for different data types in the land:

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&land=TCGA_2013_0715

Open Gene / GeneSet in Land

This opens the default view, DNA Alteration Distribution, for the gene specified:

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&land=TCGA_2013_0715&gene=egfr

This opens the default view, DNA Alteration Distribution, for the geneset specified (user must have access to the gene set):

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&land=TCGA_2013_0715&geneset=BreastCancerGenes

Open Land by Specific Grouping

This opens the default view, DNA Alteration Distribution, for the gene by specified grouping (e.g. Disease):

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&land=TCGA_2013_0715&gene=egfr&grouping=Disease

Open Specify Land View

This opens the specified land view (e.g. for a gene or a geneset

http://omicsoft.com/software/ArrayViewer/ArrayViewer.application?server=tcp://192.168.1.36:8065/RemoteServer&land=TCGA_2013_0715&gene=egfr&landview=DnaSeq_SomaticMutation.SiteDistribution

Open Land with Specific Filter