Easily assess quality control data across multiple single cell datasets
Supercells is a tool which generates a single report for multiple 10x cellranger samples - thus saving time and allowing comparative QC analysis.
It is written in Python (tested with v3.7-3.9).
Using PyPI:
pip install supercells
Clone or download the repository and navigate to the package directory, then invoke:
pip install .
Once supercells is installed it is run by invoking:
supercells -i <experiment folder>
Unless specified otherwise it will generate supercells_report.html within the input folder as well as supercells_report folder containing summarizing xlsx file and CSV with the raw data. To specify an output directory use the -o <output folder> flag
Suggestions for additional features and code contributions are welcomed