pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Hi,
I failed to run grnboost2 on a large dataset with shape 50000 cells X 28000 genes. Then I subsample the dataset to a small one and run grnboost2 sucessfully. It seems that it was caused by something related to dask:
wangjiawen2013
commented
4 months ago
Hi, I failed to run grnboost2 on a large dataset with shape 50000 cells X 28000 genes. Then I subsample the dataset to a small one and run grnboost2 sucessfully. It seems that it was caused by something related to dask:
Here is an issue on dask and hope it can help to improve pyscenic: https://github.com/dask/distributed/issues/8257
https://lightrun.com/answers/dask-distributed-array--2gb-hitting-msgpack-limit-
https://github.com/dask/distributed/issues/527