nico-sc-sp 0.0.6

Find covariation patterns between interacted cell types from spatial data.

nico

Under construction! Ready for use! Currently experimenting and planning!

Developed by Ankit Agrawal (c) Grün lab 2023

Install the NICO package using the conda environment.

conda create -n nicoUser python=3.11
conda activate nicoUser
pip install nico-sc-sp
pip install jupyterlab

Required packages built upon

By default, these packages should install automatically. But if any version conflict exists, the user can install the specific version independently.

scanpy==1.9.6
seaborn==0.12.2
scipy==1.11.3
matplotlib==3.7.3
numpy==1.26.1
gseapy==1.0.6
xlsxwriter==3.1.9
numba==0.58.1
pydot==1.4.2
KDEpy==1.1.8
leidenalg

Import the functions from the Python prompt in the following way.

from nico import Annotations as sann
from nico import Interactions as sint
from nico import Covariations as scov

Please follow the NiCo documentation here.

http://htmlpreview.github.io/?https://github.com/ankitbioinfo/nicodoc/blob/main/docs/_build/html/index.html

Please follow the Nico tutorial here.

https://github.com/ankitbioinfo/nico_tutorial

Check out more: Thanks to the following two utils packages to develop Nico.

SCTransformPy

https://github.com/atarashansky/SCTransformPy

pyliger

https://github.com/welch-lab/pyliger