Table 1.
Comparison of features between FlowKit and other FCM software libraries.
| FlowKit | flowCore (R) | Cytoflow | CytoPy | FlowCal | FlowCytometryTools | |
|---|---|---|---|---|---|---|
| Version | 0.8.0 | 2.4.0 | 1.1.1 | 2.0.1 | 1.3.0 | 0.5.1 |
| (release date) | (Oct 2021) | (Nov 2020) | (Mar 2021) | (May 20221) | (Jan 2021) | (Jan 2021) |
| Programming Language | Python | R | Python | Python | Python | Python |
| (latest version supported) | (3.9) | (4.1) | (3.72) | (3.9) | (3.8) | (2.7, 35) |
| Uses Continuous Integration | Yes | Yes | No | No | No | Yes |
| Includes tests | Yes | Yes | Yes | Yes | Yes | Yes |
| Reports test coverage | Yes | No | No | No | No | No |
| FCS file library | FlowIO | built-in | fcsparser3 | FlowIO | built-in | fcsparser |
| Supports channel gain ($PnG) | Yes | Yes, but not by default | No | No | Yes, but not by default | No |
| Supports $TIMESTEP | Yes | No | No | No | No | No |
| Supports logicle | Yes | Yes | Yes | Yes (via FlowUtils) |
Yes4 | No |
| Supports FlowJo bi-exponential | Yes | Yes | No | No | No | No |
| Supports hierarchical gating | Yes | Yes1 | No | Yes | No | No6 |
| Supports GatingML 2.0 | Yes | Yes | No | No | No | No |
| Supports FlowJo 10 workspaces | Yes | Yes1 | No | No | No | No |
1. flowCore does not include hierarchical gating or FlowJo WSP support directly, this functionality is in the related flowWorkspace library.
2. Cytoflow is installable through Anaconda.
3. Cytoflow uses an internal fork of fcsparser.
4. The FlowCal logicle function is implemented in Python as opposed to C for the other libraries in this list.
5. It is unclear which Python versions are supported, PyPI states 2.7, the README file states “python 3”.
6. FlowCytometryTools supports a CompositeGate class to combine gates but does not have an API to explicitly create gate hierarchies.