CytoPy
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burtonrj
A data-centric flow/mass cytometry automated analysis framework
I tried the conda installations step from website as well as docker image, I encounter the same numba error: `numba.core.errors.LoweringError: Failed in nopython mode pipeline (step: nopython mode backend) Storing...
I am trying to install CytoPy and I am getting this error: ERROR: Could not find a version that satisfies the requirement KDEpy==1.0.10 (from cytopy) (from versions: 0.1, 0.2, 0.3,...
Hi, do you have an updated link to the dataset. https://drive.google.com/file/d/1y6qL_7l2unDoUkNqlr9Xqubq5_sP1E14/view?usp=sharing This one is broken. It was found here: https://cytopy.readthedocs.io/en/latest/2_data.html Thanks
Hi, I wonder if I have many datasets formed as fcs from different experiments, are there any fast approaches I can use to construct the database? I cannot find the...
Not sure if this will be addressed in upcoming split of CytoPy into different tools but saving clusters takes ages. I'm running on bare metal in a fresh Conda env...
In the "inside_polygon" function of "cytopy/data/geometry.py", the performance of multi process implementation is very poor. A 10000 line of data takes nearly 30 seconds, but it only takes less than...
Improve docker documentation to explain how to start the CytoPy image with a persistent volume and connect to a MongoDB server.
I have installed conda and created a new virtual environment: `conda create --name myEnv python=3.8.5` Activate the environment: `conda activate myEnv` Installed numpy: `pip install numpy==1.19` This worked fine. But...
Hi Ross, As promised, this is the CytoPy GUI wrapper that we discussed. I'm happy for feedback or suggestions. Since this is only a single file, I suggest to include...
Hi Ross, As we discussed, this is a big pull request with many modifications and revisions we made to the code. Please let me know what you think! Best, Omer