nico-sc-sp 0.0.3

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) 2023

required packages (How to install them and their version)

conda create -n nicoUser python=3.9
conda activate nicoUser
conda install -c "conda-forge/label/gcc7" xlsxwriter
pip install gseapy, scanpy, shap, pydot, leidenalg 
pip install jupyter notebook
seaborn.__version__
'0.12.2'
scipy.__version__
'1.10.1'
matplotlib.__version__
'3.7.1'
scanpy.__version__
'1.9.3'
numpy.__version__
'1.23.5'
gseapy.__version__
'1.0.4'
numba.__version__
'0.56.4'
shap.__version__
'0.41.0'
xgboost.__version__ (only required if shap analysis is on)
'1.7.5'

from nico import Spatial_Annotations as sann
from nico import Spatial_Interactions as sint
from nico import Spatial_Covariations as scov

Creating the tutorial

will come soon ...

# Choose One

Check out more: Thanks to following two packages to built nico SCTransformPy https://github.com/atarashansky/SCTransformPy pyliger https://github.com/welch-lab/pyliger