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...
Hi All, I have followed the instructions and downloaded all the listed data from "https://pyscenic.readthedocs.io/en/latest/tutorial.html". However, in step "adjacencies = grnboost2(ex_matrix, tf_names=tf_names, verbose=True)". I got the error information like distributed.worker...
Hi all, I am getting warning /home/vtlab/.local/lib/python3.6/site-packages/numba/np/ufunc/parallel.py:365: NumbaWarning: The TBB threading layer requires TBB version 2019.5 or later i.e., TBB_INTERFACE_VERSION >= 11005. Found TBB_INTERFACE_VERSION = 9107. The TBB threading layer...
Hi all, I am getting warning /home/vtlab/.local/lib/python3.6/site-packages/numba/np/ufunc/parallel.py:365: NumbaWarning: The TBB threading layer requires TBB version 2019.5 or later i.e., TBB_INTERFACE_VERSION >= 11005. Found TBB_INTERFACE_VERSION = 9107. The TBB threading layer...
Hello! I am trying to reproduce results from pyscenic tutorial https://github.com/aertslab/pySCENIC/blob/master/notebooks/pySCENIC%20-%20Full%20pipeline.ipynb . I have an error on the step: df = prune2df(dbs, modules, MOTIF_ANNOTATIONS_FNAME) ValueError: The columns in the computed...
**Describe the bug** when I run the command:pyscenic aucell, I got an error about export loom file.I had run it at aertslab-pyscenic-0.10.0.sif and aertslab-pyscenic-0.11.2.sif.It both got the error. **Steps to...
Bumps [ipython](https://github.com/ipython/ipython) from 7.20.0 to 7.31.1. Commits e321e76 release 7.31.1 67ca2b3 Merge pull request from GHSA-pq7m-3gw7-gq5x 2794330 back to dev be343e7 release 7.31.0 0fcf2c4 Merge pull request #13428 from meeseeksmachine/auto-backport-of-pr-13427-on-7.x...
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error
**Describe the bug** When I ran pyscenic in anaconda environment, it always report "ImportError: cannot import name 'dumps_msgpack' from 'distributed.protocol.core'". How should I solve this problem? **Steps to reproduce the...
Hi, I was wondering whether you have compared the success of pySCENIC analysis at identifying "true" gene modules downstream of different normalisation methods. In particular, I am interested in whether...
For [results] How to get the list of target genes for one regulon from the output regulon.csv file of ctx https://github.com/aertslab/pySCENIC/issues/301 It is greatly interesting. Does anyone know how to...
