Setup tools

Install Neo4j

Cell Interactome is built on a graph databse Neo4j. Users first need to download/install Neo4j and make initial settings as follows.

Linux

# download executabules
wget https://neo4j.com/artifact.php?name=neo4j-community-5.5.0-unix.tar.gz -O neo4j-community-5.5.0-unix.tar.gz
tar zxvf neo4j-community-5.5.0-unix.tar.gz

# change password
neo4j-admin dbms set-initial-password ${YOUR_PASSWORD}

# execute neo4j
neo4j start

Mac/Windows

Install Neo4j with as instructed in the official document.
Change password by opening the installed Neo4j Desktop (you will be asked when opening first time)

Install Cell Interactome

You can create environment with conda and install the Cell Interactome tools as follows.

# clone files
git clone https://github.com/gagliani-lab/Cell-Interactome.git
cd cell-interactome

# setup environment
python -m venv /path/to/your/venv/cell_interactome
source /path/to/your/venv/cell_interactome/bin/activate

# install Cell Interactome
python setup.py install

Install CellInteractomeR

CellInteractomeR is an R package to play with Neo4j-based Cell Interactome graph.

# install following dependencies through devtools::install_github
devtools::install_github("ColinFay/glouton")
devtools::install_github("dreamRs/particlesjs")

# install CellInteractomeR
devtools::install_gitlab("gagliani-lab/Cell-InteractomeR")