cellenium

a FAIR and scalable interactive visual analytics app for scRNA-Seq data

Setting up

for CellO:

mkdir scratch/cello_resources
curl https://deweylab.biostat.wisc.edu/cell_type_classification/resources_v2.0.0.tar.gz >scratch/cello_resources/resources_v2.0.0.tar.gz
tar -C scratch/cello_resources -zxf scratch/cello_resources/resources_v2.0.0.tar.gz

docker-compose up
conda env create -f data_import/environment.yml
conda activate cellenium_import
# 'test_studydata' should contain data to cover all application features, but is small enough to be imported in a few minutes
make reset_database test_studydata_import
# 'normal_studydata': real life studies (i.e. with full amount of cells and genes)
make normal_studydata_import

manually executing the study data preparation jupyter notebooks

The notebooks are run in headless mode by make. To create new notebooks and explore datasets:

(cd data_import && PYTHONPATH=$(pwd) jupyter-lab)