Scanpy helper functions
A bunch of custom helper functions to help with cell type annotation and dataset integration.
Installation
Development install using
git clone git@github.com:grst/scanpy_helpers.git cd scanpy_helpers flit install -s
This is still evolving, no stable version identifiers are available. Consider adding as a git submodule to your project.
Modules
de - Differential expression
Wrapper functions around differential expression testing methods and convenience methods for integration with scanpy/anndata.
annotation - Cell-type annotation
Helper functions for clustering, annotating and subclustering.
integration - Altas-level data integration
Helper functions for standardizing data annotations across datasets and integrating them.