Installation¶

System requirements¶

We recommend to create an independent conda environment for SCRIPro. If users do not have conda, please install Miniconda first:

wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

conda create -n scripro python=3.8
conda activate scripro
conda install -c liulab-dfci lisa2
pip install scripro

Next, please download the reference files of SCRIPro from Zenodo and configure it:

lisa install hg38 oneshot hg38_scripro.h5
lisa install mm10 oneshot mm10_scripro.h5
scripro install_reference -i TF_target_RP.h5

STAGATE is designed for spatial clustering and denoising expressions of spatial resolved transcriptomics (ST) data.

To install STAGATE, use:

git clone git@github.com:QIFEIDKN/STAGATE.git
cd STAGATE
python setup.py build
python setup.py install

If you encountered with this error message:

sparse_placeholder is not compatible with eager execution.