![]() Gating tools are available at the top of SeqGeq’s Graph Window which can be opened by double-clicking on any population within the workspace. These lists of parameters can be organized into Collections for the sake of convenience and clarity:ĭouble-clicking on a Geneset will open a geneset inspector where you can investigate the genes comprising that Geneset: Genesets are groups of parameters within SeqGeq. These samples can then be subdivided into sub-populations using gates within the Cell View of a Graph Window corresponding to that sample. Populations are simply data matrices containing cells (aka events) within SeqGeq. If you’re finding data that SeqGeq won’t load we encourage you to submit a demo data-set to for further investigation and troubleshooting. In other words we try very hard to be “data agnostic”. Note: SeqGeq has been designed to accept data from all sequencing pipelines. Within the Analyze tab there’s a Navigate option, which also contains functions for loading data from your file system, or directly from Illumina’s BaseSpace application:Īnother type of data which can be dragged into the SeqGeq workspace consist of CSV lists of genes (aka Genesets). Saving, opening and quitting a workspace can be accomplished by clicking on the SeqGeq button in the top left hand corner of the workspace:ĭragging and dropping data into the SeqGeq workspace will load that data within the platform. ![]() ![]() Try adding the Boolean ribbon to the Workspace tab of your workspace: Ribbons within the tabs of the workspace can be customized to contain sections according to your prefered organization, by clicking on the Customize Ribbon icon in the top right hand corner of SeqGeq’s workspace and dragging options from there into the ribbons area of a tab. This can include nodes representing: Plugins, Statistics, Populations, Gates, or any other platforms in SeqGeq. Those samples will contain hierarchically ordered nodes representing the analysis performed on them. The Samples area of the workspace will illustrate samples within the group selected.Groups will separate out different samples from the All Samples group, and can contain gates or statistics just like an individual sample.The Genesets area of the workspace will contain sets of parameters as they are either loaded from CSV files into SeqGeq, or defined within SeqGeq based on data analyzed there.Tabs contain Ribbons with various features, grouped by common functions:.SeqGeq’s Workspace contains some general areas such as Tabs, Ribbons, Genesets, Groups and Samples. Note: Clicking Demo there will open SeqGeq in demo mode, where only the demo data which comes with the SeqGeq install can be loaded. When running SeqGeq you’ll be prompted to enter your FlowJo Portal credentials: Users can get an active license to try SeqGeq Free by signing up for a trial account within the FlowJo Portal: To sign up for, and activate a free FlowJo Portal account, visit the following site: ![]() Logging into SeqGeq requires that a researcher create an account in the FlowJo Portal environment, and an activated SeqGeq license there. Note: SeqGeq is not supported on 32bit Windows machines. After downloading the appropriate installer for your system, simply run that EXE or DMG file, and follow the instructions given, in order to put the SeqGeq software platform onto your machine. Installers are offered for both Mac (OSX 10.8+) and 64bit Windows operating systems. Installers for SeqGeq are available from the Downloads tab of the SeqGeq solutions section of the website: Researchers are encouraged to independently vet and validate their own workflows as much as possible. *Analysis performed in this tutorial should be considered as demonstration of features only. Specifically, analyses illustrated here will focus on the 6K_PBMC.csv data file. This tutorial is designed to give researchers a basic overview of the features and functions available in the SeqGeq bioinformatics analysis platform.Īll data files illustrated here are available as demo data included in the installation of SeqGeq. Basic Tutorial SeqGeq Basic Tutorial (SeqGeq v1.6.0)
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