Installation

FlowMap can be installed directly from GitHub:

pip install git+https://github.com/jingyuanhu01/flowmap.git

Minimal Dependencies

One advantage of FlowMap is that the core package uses standard scientific Python tools. The main dependencies are NumPy, SciPy, scikit-learn, UMAP, statsmodels, and matplotlib, which are installed automatically with FlowMap.

You do not need a special single-cell environment to use the core API.

Optional Single-Cell Environment

For RNA velocity workflows, it is often useful to work in a fresh environment with common single-cell tools installed.

Using conda:

conda create -n flowmap python=3.11
conda activate flowmap

Using mamba:

mamba create -n flowmap python=3.11
mamba activate flowmap

Then install FlowMap and optional RNA velocity tools:

pip install git+https://github.com/jingyuanhu01/flowmap.git
pip install scanpy anndata scvelo

Scanpy, AnnData, and scVelo are not required by the core FlowMap API, but they are commonly used for loading, preprocessing, and exploring single-cell RNA velocity data.

Development Install

If you want to edit the source code locally:

git clone https://github.com/jingyuanhu01/flowmap.git
cd flowmap
pip install -e .