grnndata (putting the grn in anndata)

Awesome gene regulatory network enhanced anndata created by jkobject & remi trimbour

grnndata works similarly to anndata. The goal was to use the .varm of anndata to store the GRN data associated with a dataset and have a formal way to work with GRNs.

grnndata is a subclass of anndata.AnnData, it enforces only that a .varm exists for the anndata

grnndata also contains multiple helper functions to work with GRNs in scRNAseq

Install it from PyPI

pip install grnndata

Usage

grnndata works similarly to anndata

How do I do if I generate a GRN per cell type?

In this context, we recommend creating a grnndata per cell type. This will allow you to store the GRN data in the .varm of the grnndata and have a formal way to work with GRNs.

How do I do if I generate a GRN per cell?

In this context, we recommend trying to merge them across a similar group of cells in some way and storing uncertainty or variance in the GRN and then creating a grnndata across this group of cells

Development

Read the CONTRIBUTING.md file.