CytoOne 0.0.2

A unified probabilistic framework for CyTOF data

CytoOne

A unified probabilistic framework for CyTOF data

Installation

You can easily install CytoOne from PyPI. Follow the following command to get started:

Create a virtual environment :snake:

So far, we have only tested the software on Python 3.9 and 3.10.

conda create -n cytoone python=3.9
conda activate cytoone 

or

conda create -n cytoone python=3.10
conda activate cytoone 

Build the package

pip

For a stable version of CytoOne, you can download and install the package via

pip install CytoOne

Local

The latest version of CytoOne will be hosted on GitHub where we constantly update features of the package. To use the latest version of CytoOne, you will need to build the package loacally.

First, you need to clone the repo to a local directory, say ./awesome_repos and cd to that folder.

Now, you should have a CytoOne folder under the awesome_repos directory. Run the following to build the package.

cd ./CytoOne
python setup.py sdist bdist_wheel

You should see a dist folder now which contains the wheel file you will need for installing the package.

cd ./dist
pip install ./CytoOne-0.0.1-py3-none-any.whl

Dependencies

With both package building strategies, the dependencies should be installed automatically. Here, we just list them out for your reference.

• python>=3.9,<3.11
• numpy<2.0
• pandas>=2.2.0
• anndata>=0.10,<0.11
• torch<2.0
• pyro-ppl<1.8.5
• seaborn
• jupyter
• ipywidgets

Tutorial :fast_forward:

Interactive Python

This assumes that you are using Jupyter notebook to run CytoOne.

Command-Line Interface (CLI)

Citation :page_with_curl:

If you use CytoOne in your workflow, citing our paper is appreciated:

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