A collection of functions for working with ISS data, including label transfer from a suspension reference and niche analysis.
show requirements
nichefinder can run on a standard computer with enough RAM to hold the used datasets in memory.
OS requirements
The package has been tested on:
- macOS Tahoe 26.3 (25D125)
- Linux: Ubuntu 22.04 jammy
Python requirements
A python version >=3.5 and <3.12 is required for all dependencies to work.
Various python libraries are used, listed in setup.py, including the python scientific stack, scikit-learn, joblib, scanpy and networkx.
nichefinder and all dependencies can be installed via pip (see below).
Optional: create a new conda environment with Python
mamba create -n nichefinder "python<3.12"
mamba activate nichefinderTo download via ssh, an ssh key must have be added to your GitHub profile.
pip install git+ssh://git@github.com/Teichlab/nichefinder.gitAlternatively, clone the repository and install with pip in two steps:
git clone <preferred way ...>
cd nichefinder
pip nichefinder .(installation time: <5 min)
Example notebooks:
(running time: <5min)
TBA