Plugin Demonstration Videos

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Plugins add a wealth of features to SeqGeq, and in doing so compliment its rich base of native analysis functionality. These plugins can be downloaded from the FlowJo Exchange on our website. The SeqGeq plugins are constantly being updated with new tools designed by the research community, allowing users to stay on the cutting edge of analysis. Each plugin may have slightly… Read more »

1.6.0 Release Notes

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Highlights Mouse-Over Information shown for both cells and genes within Graph Windows. This means that researchers can now very quickly determine the identity of individual dots in their plots with ease. We’ve also added the ability to “pin” the parameter names in GeneView plots to graphs within the Layout Editor, so that these annotations become… Read more »

Mouse-Over Annotations

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SeqGeq v1.6 and beyond now contains a mouse-over annotations feature for individual dots per cell, sample (for bulk sequencing), or per gene.     Simply drag your cursor over the plot in a Graph Window in order to see the names of dots displayed there as tool-tips. In addition to the mouse-over information, right click… Read more »

Overlays

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Overlays give researchers a powerful way to visualize comparisons between populations. On a parameter by parameter basis in univariate histograms, by binning two histograms together to reveal a bivariate dot plot, or even applying machine learning to generate derived parameters representing embedded space in a single plot. (such as tSNE and UMAP) Univariate Traditional univariate… Read more »

1.5.0 Release Notes

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Highlights Introducing a Normalization Platform – Now available in the Discovery band of the Workspace, which allows researchers to run normalization across parameter-sets in data matrices. Multi-Geneset Enrichment Analysis – Simply select multiple genesets and run the enrichment platform against a geneset library (GMT) of your choice. Opt-SNE (1) algorithm enabled! This means researchers won’t usually need to… Read more »

Normalization

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  Intro Normalization is an important consideration for any analysis, and is common to include in many sequencing datasets. Performing normalization will generate a new icon meant (generically) to indicate that an adjustment has been applied, moving (or reshaping) data:   Within the normalization platform different lists of parameters can be added. Adding a new… Read more »

VDJ Explorer

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Background Variable (V), diversity (D), and joining (J) regions of lymphocyte immune cell receptor proteins are capable of undergoing recombination, which produces a set of unique alpha and beta chain pairs (aka clonotypes), the sum totality of which is sometimes called the repertoire of T and B cell populations. Measurements of clonotype diversity give researchers… Read more »

Basic Tutorial

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SeqGeq Basic Tutorial (SeqGeq v1.6.0) This tutorial is designed to give researchers a basic overview of the features and functions available in the SeqGeq bioinformatics analysis platform. All data files illustrated here are available as demo data included in the installation of SeqGeq. Specifically, analyses illustrated here will focus on the 6K_PBMC.csv data file. *Analysis… Read more »

Combining Flow and Single Cell Sequencing

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Certain sequencing methods will utilize index sorting from flow cytometry as an upstream step in sample preparation. In these cases, many researchers don’t realize they’ve already gathered a powerful dataset which can be used to compliment the sequencing analysis. SeqGeq gives users the ability to very easily combine both fluorescence intensity information per flow channel,… Read more »

Bulk Sequencing

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While SeqGeq was designed with single-cell RNA sequencing data in mind, it can also be applied to bulk data analysis to great effect, and in many of the same ways. Though certain considerations must be made in the treatment of this type of data in SeqGeq.   Overview In bulk sequencing, the data points observed… Read more »