Installation
============

Installing ``DEVCOMSuiteR`` (R package)
---------------------------------------

.. code-block:: r

   install.packages("remotes")
   remotes::install_github("guanhaowu123/DEVCOM-Suite-R")
   remotes::install_local("xxxx/DEVCOM-Suite-R-main.zip")

Installing ``DEVCOMSuitepython`` (Python package)
-------------------------------------------------

.. code-block:: bash

   conda create -n DEVCOMSuitepython python=3.10.18 -y
   conda activate DEVCOMSuitepython

   conda install -c conda-forge \
       scanpy anndata numpy pandas scipy matplotlib \
       networkx scikit-learn squidpy==1.6.5 umap-learn -y

   pip install \
       pyliger==0.2.4 tensorflow_probability==0.25.0 \
       tensorflow==2.19.1 tf_keras==2.19.0 causaldag \
       mpart==2.2.2 pymp==0.0.6 spatial_factorization==0.0.1 \
       "git+https://github.com/willtownes/spatial-factorization-py.git#egg=spatial-factorization"

   git clone https://github.com/axelalmet/flowsig.git
   cd ./flowsig
   python -m pip install --no-deps .

   cd ~
   git clone https://github.com/guanhaowu123/DEVCOMSuitepython.git
   cd DEVCOMSuitepython
   pip install .