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Add dependencies for clarity
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kevin931 committed Dec 12, 2022
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Expand Up @@ -29,6 +29,22 @@ conda install -c normalizingflow cytomulate
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If you wish to use ``PyCytoData``, you can install separately with more instructions [here](https://cytomulate.readthedocs.io/en/dev/installation.html).

### Dependencies

Good news: we didn't have to write `cytomulate` from scratch in assembly language! This means that we will need dependencies to install it. Below is a list of packages that you will need:

- numpy
- scipy
- scikit-learn
- networkx
- matplotlib
- tqdm

Most of these are pretty standard! And even better news: the installation instructions should automatically handle all the dependency issues. If you have a problem with installation, let us know and we're happy to help!

While the above are all core dependencies, we highly highly highly highly highly recommend `PyCytoData` as well! You can get all the benefits of an integrated pipeline! But of course, for those of you who don't fancy more dependencies, we understand as well!


## Examples

We have two modes: **Creation Mode** and **Emulation Mode**. The former is probabilistic-model based simulation without the need of datasets; the latter is based on existing datasets to match as much of the existing features as possible. Here, we give two quick examples of how they work.
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