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).

📦 Installation

Using PyPI:

pip install supercells

Clone or download the repository and navigate to the package directory, then invoke:

pip install .

💻 Usage

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

Further development

Suggestions for additional features and code contributions are welcomed