Plugin Exchange
Innovative plugins and tools to upgrade your analysis in FlowJo™ and SeqGeq™
Download our Periodic Table of Plugins
Subset your sample in a specified event count
v3.3.1 published July 15, 2021
A dimensionality reduction technique similar to t-SNE
v4.1.1 published September 13, 2023
Cluster using Self-Organizing Maps
v4.1.0 published January 05, 2024
ClusterExplorer illustrates a profile of relative intensity values across parameters in flow cytometry data. *If employing FlowJo v10.10, please uninstall this plugin and use the native Cluster Explorer.*
v1.7.6 published May 17, 2023
Find anomalies in Flow Cytometry data
v2.3.2 published April 10, 2024
Delineate clusters by unsupervised nearest-neighbors grouping of biological parameters.
v4.0.5 published November 25, 2024
Configured plugins ready to go: FlowAI, FlowClean, PeacoQC, FlowSOM, Fast Phenograph, Euclid, UMAP, EmbedSOM, T-REX, CyCombine, CytoNorm, IndexSort and ViolinBox.
v2.1.0 Download for Windows 10 & 11 published April 11, 2025
Generate violin plots and box and whisker plots
v5.1.14 published December 18, 2025
Calculate Stain Index in the click of a button
v1.8.1 published March 04, 2021
A clustering algorithm that uses KNN density estimation
v1.4.1 published April 16, 2021
Automated cleaning of flow data.
v2.4 published May 04, 2021
Uses K-means clustering to create populations.
v1.0.1 published December 03, 2020
Helps correct for technical variability within FlowJo by normalizing batches of flow data
v1.2.3 published July 02, 2021
Create Interactive 3D plots, DimRedux, Unsupervised Clustering, DEG and More
v1.1.1 published January 30, 2025
Embed FlowSOM maps into 2D space
v2.2.0 published January 05, 2024
Automatically Find the Shortest Gating Strategy to a Population of Interest
v0.8.1 published October 10, 2023
Dimensionality reduction, analogous to tSNE or UMAP. This algorithm is used as visualization for high parameter datasets.
v0.2 published February 05, 2020
Configured plugins ready to go: FlowAI, FlowClean, FlowSOM, CytoNorm, IndexSort and ViolinBox.
v1.1 Download for MacOS published May 13, 2023
Automatically gate wells from BD index-sorted data
v3.0.8 published October 31, 2024
Correct for batch effects between combined samples directly within SeqGeq
v1.0.10 published June 12, 2023
Cytometric Bead Array kit analysis
v5.2.2 published November 17, 2023
Measure the quality of clustering in n-dimensional space using two statistical methods - ClustRCheck and Taylor Index.
v0.9 published October 10, 2023
Automatically gate categorical parameters.
v2.6.1 published December 03, 2020
Automatically name subsets according to Astrolabe Diagnostics population annotations in FlowJo.
v0.6 published September 09, 2019
Population hierarchies in an R based Shiny App.
v0.1 published April 30, 2020
Deep-Learning Cell Classification
v1.5 published May 30, 2019
Seurat pipeline developed by the Satija Lab
v5.0.2 published July 01, 2024
An R based quality control algorithm to remove abnormal events from flow data!
v1.5.0 published August 30, 2023
Pseudotime project and scRNA-Seq analysis
v4.3 published April 04, 2023
Correlation graphs and statistics.
v0.4.1 published September 11, 2023
Visualize population hierarchies and expression patterns across those trees, in network visualization maps, using this Shiny App based plugin.
v0.3 published September 06, 2020
PHATE (Potential of Heat-diffusion for Affinity-based Trajectory Embedding)
v1.0.0 published September 08, 2021
User-guided automated gating analysis.
v0.5.1 published December 09, 2022
Visualize your high dimensional data in fewer dimensions.
v2.0.0 published September 29, 2025
Calibrate samples using a standard curve
v1.0 published May 30, 2019
Use a simple rubric for population identification to automate the process of labeling clusters.
v0.1 published November 03, 2020
Robust Integration of Single-Cell Cytometry Datasets
v1.0.2 published June 28, 2023
A utility tool for demultiplexing samples from single-cell RNA sequencing experiments.
v1.1 published November 16, 2020
A tool for visually exploring your BD FACSDiscover™ imaging data in FlowJo!
v2.0.15 published April 11, 2025
Single-Cell Immune Repertoire Profiling
v4.3 published October 17, 2023
An Algorithm that attempts to mimic the way an expert flow cytometry analyst interprets and adjusts gates in 2-dimensional plots.
v1.2 published August 10, 2023
Dimensionally reduce, cluster and identify areas of difference between two user specified experimental conditions.
v1.2.2 published January 05, 2024
Support Vector Machine (aka "SVM") automated gating tool for FlowJo.
v0.1 published January 29, 2020
A plugin for importing BD FACSDiva™ Software experiments into FlowJo.
v2.0 published January 08, 2021
Fix mismatching parameter names in template workspaces.
v0.3 published November 20, 2020
Merge CSV files into data using SeqGeq, and retain population annotations.
v0.3.1 published February 21, 2020
Dropout imputation using a low-rank approximation
v0.1 published May 30, 2019
A tool for converting FlowJo v9 .jo files into FlowJo v10 wsp files.
v0.2 published November 03, 2021
Impute the dropout values in scRNA-seq data
v1.0 published May 31, 2019
Premessa is a tool to edit the parameter and/or stain names of an FCS file if these were incorrectly written from the cytometer.
v1.0.3 published May 16, 2025
The FlowJo Mutual Nearest Neighbors Plugin is a tool to correct batch processing variation in flow cytometry data.
v1.0.0 published November 06, 2023
Automatically identify singlets, multiplets and debris.
v1.2.6 published December 13, 2024
flowCut is a tool for separating quality events in FCS data from outlier events to achieve a more uniform distribution of data.
v1.0 published February 12, 2024
Automatically identify populations in different cell cycle phases.
v1.0.2 published June 26, 2025
Utilize FCS data captured from Rosetta Calibration beads to calibrate size measurements of small particles.
v1.0.0 published February 24, 2023
A tool to help determine the best voltage for acquisition that will optimize the stain index (SI) of cells stained with a reference reagent for each detector.
v1.0.0 published August 14, 2024