Release Notes

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Overview SeqGeq is a standalone desktop application that allows you to explore your single-cell RNAseq data with an intuitive drag-and-drop interface. SeqGeq puts cutting-edge bioinformatics tools in your hands with a user-friendly interface that makes it easy to extract gene sets, produce publication-quality graphics, and analyze complex data rapidly. After sample preparation, sequencing, and primary… Read more »

Approach—Initial Analysis Overview

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When first approaching a single-cell RNA-seq dataset, the task can be daunting. You are faced with tens of thousands of genes (or splice variants), and as many cells or more. From here you have two possible starting points in SeqGeq: Create gene sets to organize and manage parameters. Gate populations of cells to define subsets…. Read more »

Pivot Window

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Also known as Gene view, the Pivot function in SeqGeq is a robust and unique feature. This feature allows you to “flip the table” on a large set of genes, so to speak, and look at those gene parameters as events within the Graph window. Note: This function is not a simple axes transform; it is more… Read more »

SeqGeq™ Documentation

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SeqGeq™ (SEEK-GEEK) helps you extract insight from the individuality of single-cell gene expression. Each cell is a complex, unique individual, containing between 50,000 and 300,000 transcripts. SeqGeq™ analyzes gene expression data, particularly from single-cell RNA sequencing (scRNA-seq). SeqGeq was built by and for scientists, with powerful data reduction tools to help you discover, cluster, and… Read more »

Gene Sets

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Gene sets (hallmark gene lists, or gene tables) are lists of genes known to be related or expressed in the same cell population. The term simply refers to a list of genes, usually associated with a particular biological function or cell population. The Gene Set is a fundamental concept of SeqGeq, which helps to organize… Read more »

Glossary

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Some of the following terms are industry-standard, and some have meanings specific to SeqGeq. Analytical Gene Set A list of genes created in Gene view, and which also has a geometric/threshold definition in Gene view. See Gene View. Attributes Additional descriptive data about a gene set, input data to SeqGeq, or output data from SeqGeq. Cell… Read more »