FlowJo offers a number of advanced features for automating analyses or facilitating analysis of more complex data.
Archival Cytometry Standard (ACS) are container files that compress workspaces, FCS data files, and plugin outputs into a single compressed .zip file, helpful for archiving, sharing, or working with remote data storage.
Templates are an excellent way to expedite data analysis by applying a previous analysis to new data. A template contains the groups, gates, and statistics without the associated FCS files for re-use.
Embed: Forward propagate clustering or dimensionality reduction results to new files with the same parameters.
Cluster Explorer: Display line charts, bar charts, heat maps, and dimensionality reduction plots of clustered data in FlowJo without the use of a plugin.
MEM – Marker Enrichment Modeling (MEM): Re-name clusters automatically and quantitatively based on their marker expression with a human- and machine-readable label.
Spectral similarity scores: Calculate the cosine index for acquired data to evaluate reagent choices made in panel design based on data from your specific instrument and experimental conditions.
Auto-Quad gates: Automatically create quads and rectangle gates based on range gates, bi-sector gates or the data itself.
Clone gates: Gates with the same name can now be linked together as ‘clones’ so that their position is synchronized.
R-tools provide additional functionality for complex data analysis.
Dimensionality reduction is a means of creating mathematically derived parameters that represent the collected parameters holistically, providing excellent visualization of high-dimensional data or clustering results.
Taylor Index: A statistic used to asssess the goodness of a clustering result.
Command line FlowJo is a means of running FlowJo “headlessly” without human intervention.
Script Editor is a tool that allow for users with JavaScript skills to interact programmatically with FlowJo to produce automation routines.
De-identification utility is a stand-alone tool that allows users to strip identifying information out of FCS files to preserve privacy.
