Chodkowski M. et al., A ligand-receptor interactome atlas of the zebrafish. iScience 2023, doi: 10.1016/j.isci.2023.107309 URL: https://pubmed.ncbi.nlm.nih.gov/37539027/

To download it you can go to the Github website and click on the Download button.

However if you have a git tool install then you can clone this using a simple command.

git clone https://github.com/DanioTalk/daniotalk

There are two ways to install DanioTalk:

• using docker (Linux, Windows, MacOs)
• without docker (Linux only)

If you want to use docker go to the docker website and install it

https://docs.docker.com/desktop/install/

For the purpose of this tutorial we will use the CLI version of Docker.

If you have a poor internet connection or you want to build the up-to-date docker image with up-to-date assets files, then you can go into the downloaded/cloned repository:

cd <path/to/repository/on/your/machine>
docker build -t mlchodkowski/daniotalk:latest .

Now the docker image creation will begin.

If you have good internet connection then you can pull the image from dockerhub:

# image location: https://hub.docker.com/repository/docker/mlchodkowski/daniotalk
docker pull mlchodkowski/daniotalk:latest

Enter the directory daniotalk. From this directory execute the following commands:

cd Data/
./fetch_data.sh
cd ..

Now you have all the files downloaded and you can run

python create_pairs.py

Requirements libraries are provided in the requirements.txt file.

python -m pip install -r requirements.txt

If you want to use docker do the following:

# If you already have a running container and want to remove it just exec `docker rm -f daniotalk`
docker run -itd --name daniotalk --entrypoint=/bin/bash mlchodkowski/daniotalk:latest
docker exec -it daniotalk bash
# You should see something like this at the beginning of the line (it means that container was created successfully)
# docker@158db1d9cfa1:/daniotalk$

python create_pairs.py

If you have the software installed locally (not using docker) then you have to just cd into the cloned repository.

cd <path/to/repository/on/your/machine>
cd Data/
bash fetch_data.sh # If you already have the files downloaded then you can skip this step
cd ..
python create_pairs.py

docker@ae0aac9f01b5:/daniotalk$ python3 create_pairs.py

______            _     _____     _ _
|  _  \          (_)   |_   _|   | | |
| | | |__ _ _ __  _  ___ | | __ _| | | __
| | | / _` | '_ \| |/ _ \| |/ _` | | |/ /
| |/ | (_| | | | | | (_) | | (_| | |   <
|___/ \__,_|_| |_|_|\___/\_/\__,_|_|_|\_
04:27:58 [INFO 🐠]: Fetching ZF and HUMAN orthology data...
04:28:01 [INFO 🐠]: Loading receptors and ligands...
04:28:01 [INFO 🐠]: Joining association files...
04:28:02 [INFO 🐠]: Reducing redundant records; aggregating frames...
04:28:03 [INFO 🐠]: Joining human orthology...
04:28:03 [INFO 🐠]: Loading Matrisome annotation
04:28:05 [INFO 🐠]: Adding Matrisome annotation
04:28:05 [INFO 🐠]: Adding conservation scores
04:28:08 [INFO 🐠]: Loading data from IID...
04:28:10 [INFO 🐠]: Creating pairs from IID data...
04:28:17 [INFO 🐠]: Creating every possible ligand-receptor pair...
04:28:19 [INFO 🐠]: Creating list of pairs from STRING...

If you used the software locally (not installed using docker) then the Database.xlsx file will be saved in the Database/ directory.

However if you used docker then you have to copy the results from the container. First exit the container

# docker@158db1d9cfa1:/daniotalk$
exit

Then from the powershell or any other terminal execute this command:

docker cp daniotalk:/daniotalk/Database/Database.csv <path/to/save/location>
# Example
# docker cp daniotalk:/daniotalk/Database/Database.csv C:/Users/user1/Desktop/

To remove the running container:

docker stop daniotalk
docker rm daniotalk

Congratulations! Now you have successfully executed the scripts using Docker.

DanioTalk repository has a directory Scripts containing 4 scripts written in R. You can open this scripts and edit their content in comment-highlighted sections (you can edit input filenames and other parameters). These scripts need a dependency files which you should put next to the script itself (in the same directory).

1. Ligand-Receptor finder for DE genes (Scripts/script_v14_DanioTalk LR finder for DE genes.R)
2. Ligand-Receptor finder for all expressed genes (Scripts/script_v15_DanioTalk LR finder for all expressed genes.R)
3. Group visualizer (Scripts/script-circ_v3_2 group visualizer.R)
4. Multiple group visualizer (Scripts/script-circ_v6_LR multiple group visualizer.R)

1. For script_v14: Excel file with your singleCell or bulk RNA-seq data with the following columns (Cell type, Gene, FC, P-value) - default name: Data Sheet.xlsx. Example:

   Cell type        Gene        FC        P-value
   Celltype1        ndr2        7.55    0.00E+00
   Celltype1        spaw        7.16    0.00E+00
   Celltype1        ndr1        7.16    0.00E+00
   Celltype2        ackr3a        7.16    0.00E+00
   Celltype2        ackr3b        7.16    0.00E+00
   Celltype2        ackr4a        7.16    0.00E+00
   

   • Generated database file (Database.csv) from Database/ directory
   • aliases.txt, human_orthos.txt files from the Data/ directory
   • Plasma ligands_expt.xlsx and Plasma ligands_predicted.xlsx from Assets/ directory
   • Note! If you're using docker you can get these files using docker cp command just like when you were copying the Database.csv file.

2. For script_v15: Excel file with your singleCell or bulk RNA-seq data with the following columns (Cell type, Gene, Expression) - default name: Data Sheet.xlsx. Example:

   ```
   Cell type        Gene        Expression        
   Celltype1        ndr2        3.00    
   Celltype1        spaw        0.09    
   Celltype1        ndr1        0.04    
   Celltype2        ackr3a        0.45    
   Celltype2        ackr3b        0.31    
   Celltype2        ackr4a        0.30    
   ```
   

   • Generated database file (Database.csv) from Database/ directory
   • aliases.txt, human_orthos.txt files from the Data/ directory
   • Plasma ligands_expt.xlsx and Plasma ligands_predicted.xlsx from Assets/ directory
   • Note! If you're using docker you can get these files using docker cp command just like when you were copying the Database.csv file.

3. • Resulting-ligand-receptor-pairs.xlsx generated by first or second script (Ligand-Receptor finder)

4. • Resulting-ligand-receptor-pairs.xlsx generated by first or second script (Ligand-Receptor finder)

You can just copy all the scripts into new directory and add dependency files. From this directory you can either cd into it and run the scripts using command

Rscript <script-name>.R

Or you can open RStudio, then open script, use setwd to set working directory to the path containing scripts & assets files and click on Source to run whole script or click Run to run single line at the time.