sciduck 0.5.5

single cell data analyis unification and communication toolkit

sciduck: single cell data quality control toolkit

sciduck provides a transparent framework for single cell/nuclei quality control and annotation. The package was built following anndata and scanpy to easily fit into related workflows. It provides tranparency to single cell analysis pipelines for reproducible data analysis and annotation. The Python-based implementation efficiently deals with datasets of more than one million cells.

Tutorials:

Quality Control

In the Quality Control tutorial we showcase how to perform various range and group contraints.

Plotting

In the Plotting tutorial we show how to use the sciduck plotting functions to identify quality control cuttoffs.

Annotation Table (Taxonomy)

In the Annotation Table tutorial we show how to build an annotation table for use in taxonomy development. Typically what is hosted on google sheets at the Allen Institute.

Documentation

Read the docs

Installation

pip install sciduck