tivelo 0.0.5

single cell velocity analysis

TIVelo

a tool to be published on Nature.

Installation

tivelo requires Python 3.8 or later. We recommend to use Miniconda.

conda create -n tivelo python=3.9 conda activate tivelo

We have published the tivelo package on PyPI. To ensure a smooth and stable installation process, we recommend installing large dependencies separately before installing tivelo in a conda environment.

pytorch

conda install pytorch torchvision torchaudio pytorch-cuda=12.1 -c pytorch -c nvidia -y

numba

conda install numba To enable CUDA GPU support for Numba, install the latest graphics drivers from NVIDIA for your platform. (Note that the open source Nouveau drivers shipped by default with many Linux distributions do not support CUDA.) Then install the CUDA Toolkit package.

For CUDA 12, cuda-nvcc and cuda-nvrtc are required:

$ conda install -c conda-forge cuda-nvcc cuda-nvrtc "cuda-version>=12.0" -y For CUDA 11, cudatoolkit is required:

$ conda install -c conda-forge cudatoolkit "cuda-version>=11.2,<12.0" You do not need to install the CUDA SDK from NVIDIA.

scanpy

conda install -c conda-forge scanpy python-igraph leidenalg -y

scVelo

pip install -U scvelo Parts of scVelo (directed PAGA and Louvain modularity) require (optional): pip install igraph louvain Using fast neighbor search via hnswlib further requires (optional): pip install pybind11 hnswlib

tivelo

pip install tivelo

Jupyterlab

To run the tutorials in a notebook locally, please install: conda install jupyterlab -y