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.