Installation Guide

Miniconda3

We recommend using Miniconda3 or Anaconda as the environment manager. Make sure conda is installed.

Creating the Cisformer Environment

To get started, copy requirement.sh to your local server and run:

conda create -n cisformer python=3.10
conda activate cisformer
bash ./requirement.sh

Alternatively, you can install dependencies manually:

conda create -n cisformer python=3.10
conda activate cisformer
conda install numpy=1.23
conda install pytorch=2.2.1 torchvision=0.17.1 torchaudio=2.2.1 pytorch-cuda=12.1 -c pytorch -c nvidia
conda install -c conda-forge accelerate==0.22.0
conda install -c conda-forge scanpy python-igraph leidenalg
pip install ninja
pip install flash-attn --no-build-isolation
pip install torcheval
conda install tensorboard
conda install pybedtools

Install from PyPI

pip install cisformer