pySCENIC
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aertslab
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 regula...
``` /home/user/anaconda3/envs/pyscenic_env/lib/python3.6/site-packages/arboreto/algo.py:214: FutureWarning: Method .as_matrix will be removed in a future version. Use .values instead. expression_matrix = expression_data.as_matrix() creating dask graph 48 partitions computing dask graph distributed.protocol.core - CRITICAL -...
[BUG]
When I was running: df = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FNAME, client_or_address = 'custom_multiprocessing', num_workers = 6) on my Windwos laptop with 64G RAM and 16 threads i7 CPU it turned out...
**Describe the bug** Running `grnboost2(ex_matrix, tf_names=tf_names, verbose=True)` from the demo example results in error **Steps to reproduce the behavior** 1. Command run when the error occurred: ```python grnboost2(ex_matrix, tf_names=tf_names, verbose=True)...
**Describe the bug** from pyscenic.transform import df2regulons is giving me an error and i'm unable to import it. **Steps to reproduce the behavior** 1. Command run when the error occurred:...
Bumps [urllib3](https://github.com/urllib3/urllib3) from 1.26.4 to 1.26.5. Release notes Sourced from urllib3's releases. 1.26.5 :warning: IMPORTANT: urllib3 v2.0 will drop support for Python 2: Read more in the v2.0 Roadmap Fixed...
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Hi @All, The human data to run the pyscenic display below error: The pyscenic can generated the auc matrix well but the binary matirx. the error showing below: Base on...
Hi @cflerin ! I have few questions regarding "direct target identification" I was wondering if you could specify in what step this happens? I followed this tutorial : https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Full%20pipeline.ipynb I...
Hi everyone, I am trying to use the pyscenic workflow to infer grn on my 10X scRNA dataset. I completely followed the demonstration workflow posted on SCENICprotocol cancer data sets...
I have been running pyscenic ctx for over 5 days. My unfiltered loom file contains ~7k cells. How long does this step typically take? I am running it from a...
Hi, I am running pySCENIC following this vignette: https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Integration%20with%20scanpy.ipynb Everything runs smoothly until the step of creating loom file, that is, the following snippet of code: export2loom(df_tpm.T, regulons, LOOM_FNAME, cell_annotations=adata.obs['cell_type'].to_dict(),...
