Installation

Python Dependencies

The following dependencies will be installed along with pianno. .. code-block:: python

anndata==0.8.0 scanpy==1.9.1 squidpy==1.2.2 opencv-python==4.5.5.64 rpy2==3.4.5 scikit-image==0.19.2 scikit-learn==1.0.2 scipy==1.8.0 protobuf==3.20.3 numpy==1.19.5 keras==2.6.0 nni==2.5

R Dependencies

r-scran==1.28.2
r-saver==1.1.2

Pianno uses the R packages SAVER and scran in preprocessing for noise reduction and size factor calculation, respectively. These two R packages will be automatically installed during the corresponding analysis in Pianno.

Installation

Downloading Pianno code from https://github.com/yuqiuzhou/Pianno

# create an environment called Pianno
conda create -n Pianno python=3.9.10

# activate your environment
conda activate Pianno

# install R in the Pianno environment
conda install -c conda-forge r-base=4.1.1

# install tensorflow and tensorflow-probability
# ensure the version 2 of tensorflow
pip install tensorflow-gpu==2.6.0
pip install tensorflow-probability==0.14.0

# install pianno from PyPi
pip install pianno

import pianno as po