Scripts for analyzing and annotating data from the MACA project.
Click on the button labeled "Clone or download" and select "Download ZIP". Unzip the archive and you should be able to open MACA_Plate_Notebook.Rmd in RStudio.
If you have git installed and you feel adventerous, you can install this repository using the command:
git clone https://github.com/czbiohub/maca
From then on you can download updates using git pull origin master. This might overwrite modifications you have made to your local copy, so we recommend making a copy of the scripts you are using.
The following commands are only necessary for installing the Python scripts in this repository—they are not needed for using Seurat.
cd maca
pip install -e .
Analysis requires R 3.4, the Java JDK, and the Seurat package. We also recommend installing RStudio for a nicer interface to R. Once you have installed R you can install Seurat using the command:
install.packages('Seurat')
Open download_script.R and modify the variable tissue_to_download to the tissue you are interested in. You can find the list of tissue names in metadata/MACA_Metadata.csv. Also change the value of root_dir to the location that you downloaded this repository. Run this script to download and unzip all of the available 3-month plate data for the tissue of interest.
Open MACA_Plate_Notebook.Rmd in RStudio, modify rootdir and tissue_of_interest as before, and step through the instructions. If you encounter problems, you can email the MACA mailing list, open an issue on GitHub, or ask the Slack channel.