In Omicsoft's Lands (ImmunoLand and OncoLand), we have pre-configured over 40 views for different data types, including RNA-Seq, DNA-Seq, miRNA-Seq, Copy Number Variation, Gene Expression Chip, Protein Expression, Methylation and hundreds of clinical measurements. While we design our Lands to be extremely powerful in providing visualizations with customizable gene, sample and project filters along with customizable graphical designs, we acknowledge that it sometimes takes time to explore the data. For some of our customers, admin/super user want to configure their company or group specific views. Or, users in a specific research group may want to set customized views that are most commonly used for a specific disease or project. All these customization can be done through the Land custom view format.
How many steps does it take to display the expression of gene POLR3A at difference stages of systemic sclerosis comparing to normal control in study GSE58095? To draw the plot like the one below, the use needs to search the gene POLR3A, click on Expression | Expression Intensity view, filter project GSE58095, change grouping to disease category and make sure the color and scale are of the preferred settings.
After the user has made it to this view and feels it can be potentially very informative for his or her project, the user can save the view:
Furthermore, if the user wants to share to view with the whole team and would like to replicate this query for other genes or projects, the user can ask the admin to create custom views. To see how to create customer views in land, please check out our wiki page: Custom Views in Land or contact us. As a standard user, the query can be set up as Custom Views, or even be grouped into a selection of custom views into specific project folder, like this one for Scleroderma Projects: