SeqGeq™ is a collaboration between Illumina, Inc. and FlowJo, LLC which has 19+ years experience in single cell data analysis.

SeqGeq™ provides powerful tools for exploring single-cell next-gen sequencing data with an intuitive drag-and-drop interface that makes it easy to get up-to-speed. 

Identify and explore sub-populations with tools like tSNE and PCA, identify differentially expressed genes and generate publication-ready figures with a few mouse clicks.

Import and analyze any gene expression data or list of genes and share your entire analysis with one file.

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 April 12th   May 10th 

Built for and by Scientists

Single-Cell Sequencing

SeqGeq™ analyses data from RNA-Seq and single-cell RNA sequencing (scRNA-seq), which provides the expression profile of individual cells using next-generation sequencing (NGS) technology to provide up to whole transcriptome analysis. 

Populations & Gene Sets

With its powerful data reduction tools, SeqGeq™ helps you discover populations and their relationships as well as examine and create gene sets.

Visualize & Communicate

Statistic heatmapping on individual cells, summary heatmaps, and drag and drop report editors help you rapidly summarize and communicate your results.


SeqGeq™ is available for download on Mac and Windows!

FlowJo University

Check out the new SeqGeq™  modules in FlowJo University!