Installation guide

The scmmib package can be installed via following 2 steps:

1. Preparing the envrionment. - Option 1:/ install minimum dependencies by pip.

1pip install scib scglue scanpy

  • Option 2 (recomended): install all dependencies with conda.

1conda env create -f scmmib_env.yml
2conda activate scmmib

  1. Install scmmib package.

1# download SCMMIB
2git clone https://github.com/bm2-lab/SCMMI_Benchmark
3# set dir to folder
4cd SCMMI_benchmark
5pip install .

  1. Test the installation in python

1import scmmib
2scmmib.__version__

Note

  • A bug may occur for graph LISI metrics as follows:

    “FileNotFoundError, [Errno 2] No such file or directory: ‘/tmp/lisi_svo3el2i/graph_lisi_indices_0.txt’””

    The related GitHub issue in scib project is here and a posssible solution .