The PeacoQC plugin for FlowJo ! The Peak Extraction and Cleaning Oriented Quality Control (PeacoQC) plugin performs quality control on cytometry data, evaluating the sample signal for regions of irregularity. This algorithm can help remove clogs and changes in flow rate, helping clean up the data. The algorithm identifies density peaks within each parameter and… Read more »

Cluster Explorer


IntroductionCluster Explorer is a FlowJo plugin. The tool creates an interactive cluster Profile graph, heatmap, and displays the cluster populations on a tSNE/UMAP plot. The plots are dynamic, can be copied to the clipboard or FlowJo Layout, and allow the user to select populations in one view and highlight the selected population in the other… Read more »



How-to-UMAP Uniform Manifold Approximation and Projection (UMAP) is a machine learning algorithm used for dimensionality reduction to visualize high parameter datasets in a two dimensional space. (1) The UMAP plugin will run with both FlowJo and SeqGeq bioinformatics data analysis platforms. Note: The UMAP plugin for FlowJo requires requires a 64bit OS. This is due… Read more »

Batch Using Iterate by Keyword


For many types of batch reports, simply iterating by the Sample or Panel are the easiest option, but in some cases we need to be more specific about which samples to include in the batch reports. In this case we can use iterate by keyword. Iteration by keyword uses a pair of keywords to specify… Read more »


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Introduction PhenoGraph is a clustering algorithm that robustly partitions high-parameter single-cell data into phenotypically distinct subpopulations. First, it constructs a nearest-neighbor graph to capture the phenotypic relatedness of high-dimensional data points and then it applies the Louvain graph partition algorithm to dissect the nearest-neighbor graph into phenotypically coherent subpopulations. The PhenoGraph algorithm has been implemented… Read more »

Sample Quality Check


The Sample Quality Badge can be used to simply access the quality of each of the samples using the metric discussed in Sample Properties. This check can be performed by simply double clicking on the circle to the left of the file name. The color of the dot will indicate the relative quality of the… Read more »

AutoSpill Compensation


AutoSpill is a new algorithm for calculating spillover and producing a compensation matrix developed and incorporated into FlowJo v10.7 in collaboration with researchers from the Vlaams Instituut voor Biotechnologie in Belgium and the the Babraham Institute in Cambridge, UK. This form of gate-less compensation removes some of the requirements of traditional compensation making compensation faster and simpler…. Read more »

10.6.2 Exhaustive Release Notes


Updates Functional within Mac OS 10.15 (Catalina) – Requests permissions to access files and folders Update to use Java version 9 Increased absolute value of negative option for scaling in BiExponential Include No More Than option in Export/Concatenate menu is being updated for full functionality Open Original Graph option from the Layout Editor now opens… Read more »

10.6.2 Release Notes


New Features: Fix issues in Mac OS 10.15 (Catalina) Update to use Java version 9 Improved support for JO workspace reading Performance enhancing features Multigraph overlaid plots in the Layout Editor now allow for additional plot type customizations More Info For more about features and a list of known issues, see the exhaustive release notes.

Dimensionality Reduction


Visualize all of your parameters in a single 2D approximation! Dimensionality Reduction has become a popular way of visualizing high parameter datasets. Most of the dimensionality reduction algorithms for FlowJo are available as plugins on FlowJo Exchange, hosting these tools in plugin form allows for very rapid deployment and development. UMAP TRIMAP PCA EmbedSOM PaCMAP… Read more »