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 »

Analysis Workflows

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There are at least as many different possibilities when planning an analysis strategy in SeqGeq, as there are cell types to explore. In the following pages we detail some broad possible directions a researcher might take, and considerations involved for each.   Overview The tack used for a given analysis should be tailored to the… Read more »

Clustering Platform

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Whether you’re aiming to apply KMeans or KNearest Neighbors to your data – We can cluster that! SeqGeq contains a Classification platform available from the Discovery band within the workspace.   KMeans Clustering   To run KMeans, simply select your population or sample of interest from within SeqGeq’s workspace, and click on the Classification button within the… Read more »

1.4.0 Release Notes

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Highlights Introducing a Clustering Platform – Now available in the Discovery band of the Workspace, which allows researchers to run KMeans clustering and KNearest-Neighbors (KNN) classification. Genes illustrated in the Pivot Window (i.e. Gene View) can now be selected and filtered in the top left hand corner of the Graph Window. This allows researchers to focus… Read more »

Downsample

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The Downsample platform reduces the number of events in a data matrix by generating a subpopulation containing cells distributed regularly or randomly throughout the selected parent population. The Downsample feature is available once a population has been selected, from within the Discovery section of SeqGeq’s Analyze tab of the workspace:   Why Downsample? Downsampling can… Read more »

Latest Release

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Our latest version is SeqGeq 1.7.0. What’s New The new update includes the following major improvements: Issues with the “Save” function have been fixed. This extends to the auto-save dialog created when closing a workspace. It should no longer be necessary to always use the “Save As” function and make successive versions, or save excessive… Read more »

Multigraph Color Mapping

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Illustrating the expression of many genes within a plot of interest was a tedious process, until now! Multigraph color mapping is a feature in SeqGeq, which illustrates many copies of a chosen plot from the Layout Editor, and color maps each by a different gene selected. This is particularly useful for exploring different aspects of dimensionally… Read more »

1.3.0 Release Notes

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Highlights Introducing the Geneset Enrichment platform, accessible by right clicking on a gene set. Multigraph Color Mapping  feature in “Multigraph Overlay” section of Layout Editor plot right click drop down menu. New multi-omics demo data set for Systemic Lupus Erythematosus (SLE) provided by Accelerating Medicines Partnership consortium. Proxy credentials dialog now available when no internet… Read more »

Gene Set Enrichment

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Gene Sets are a vital part of any sequencing analysis. These are parameter collections that can represent a wide variety of biological states. Interpreting the meaning of a given gene set within the context of a data-set or experiment can be the most challenging aspect of an analysis. Gene set enrichment is a process for… Read more »

FAQ

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There are a growing number of sites performing single cell sequencing experiments, and with them come lots of great questions. Here are a list of some commonly encountered technical queries, regarding analyses in SeqGeq.   The Good News: Questions or issues for which we have a quick solution. Why do I need a free FlowJo Cloud… Read more »