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.
- Native 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.
- Autofluorescence extraction in traditional (gate-based) compensation: Use an unstained cell data file and true zero as the background value to model autofluorescence for extraction.
- 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.