Installation Guide

You can easily install PyCytoDR from either conda or PyPI. We recommend conda for its easy environment management, but you can of course use PyPI if you prefer. Just follow the instructions below and you are good to go!

Conda

You can install our package on conda:

conda install pycytodata -c kevin931 -c bioconda

Our conda package is published here.

PyPI

You can also install our package on from PyPI:

pip install PyCytoData

Our PyPI package is published on this page.

Dependencies

We try to make this package as lightweight as possible. Thus, as of now, we only depend on three packages:

  • fcsparser

  • pandas

  • numpy >= 1.20

fcsparser and pandas are used for handling benchmark datasets and their associated fcs files. We use numpy for all computations and preprocessing.

Python Versions

We currently are tested on the following versions of Python:

  • 3.9

  • 3.10

  • 3.11

  • 3.12

However, we try to make PyCytoData as widely supported as possible. In fact, we in theory support any Python version all the way back to 3.7.

Note

Newer Version of Python We in theory should support newer versions of Python as well, such as Python 3.13. However, one of the optional dependencies CytofDR below depends on numba, which does not support 3.13. Therefore, this version does not currently pass our CI pipeline. If you do not plan on using CytofDR, feel free to use the newest version of Python available.

Optional Dependency

If you wish to perform dimension reduction (DR), you can install CytofDR and have it integrated into this package. We know that DR is a pretty common workflow, but we didn’t make it mandatory because CytofDR depends on a large number of DR packages, which makes the dependency unnecessarily complex if one does not wish to perform DR. To install CytofDR, you can run the following:

pip install CytofDR

Or, with conda:

conda install -c kevin931 cytofdr -c conda-forge -c bioconda

For detailed documentation on CytofDR installation, which can get quite tricky if you want to use its own optional dependencies such as SAUCIE and GrandPrix, you can visit its Installation Guide.