FlowKit
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whitews
A Python toolkit for flow cytometry analysis supporting GatingML and FlowJo workspaces
Documentation says that `subsample_events()` returns a `numpy` array. It does not return any object, nor it changes the dataset attribute in place. See the appropriate code: https://github.com/whitews/FlowKit/blob/e049a56973bed9b4aa8455d743f4d2e9f4440399/flowkit/_models/sample.py#L370-L417
The networkx package is used to process gates in order of their dependencies (i.e. parent gates processed before their children). This is done through the `topological_sort` function. Unfortunately, this means...
Hi, thanks for the very useful package! I recently encountered an unexpected behavior while loading a workspace instance. In particular it appears that the gating hierarchy tree is incompletely loaded....
Hello, I want to get the frequencies of some populations of my samples via flowkit. I already worked several times with different samples and gating-strategies, but never had such an...
The group concept in a FlowJo workspace is somewhat odd. Each sample can have only one gate tree and it is tied to the sample regardless of which groups the...
Given a Sample instance, generate a set of transforms for every channel. The set would create linear transforms for scatter & time channels and logicle transforms for fluorescence channels. The...
**Is your feature request related to a problem? Please describe.** I would like to use FlowJo 10.0 with a FCS 3.2 format file. Currently FlowKit seems to be only supporting...
# FlowKit Community Input Hello FlowKit users! This issue is a way to get feedback from the community on specific aspects of FlowKit development. GitHub doesn't have a good way...
Add `source` kwarg to `Workspace.get_gate_events` to retrieve gated events in various stages of preprocessing (original, compensated, transformed). This option would be consistent with `Sample` methods. Also, this is made possible...