nico-sc-sp 0.0.4

Find covariation patterns between interacted cell types from spatial data.

nico

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

Developed by Ankit Agrawal (c) Grün lab 2023

required packages (How to install them and their version)

conda create -n nicoUser python=3.11
conda activate nicoUser

Required packages are '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'

```python
#Import the functions in following way:
from nico import Annotations as sann
from nico import Interactions as sint
from nico import Covariations as scov

Creating the tutorial

Please follow the Documentation here.
http://htmlpreview.github.io/?https://github.com/ankitbioinfo/nicodoc/blob/main/docs/_build/html/index.html

And Tutorial here.
# Choose One

Check out more: Thanks to following two utils packages to develop nico SCTransformPy https://github.com/atarashansky/SCTransformPy

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