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 pySCENIC team, Thank you for providing a great tool. I am running pyscenic using my original zebrafish data. However, I got an empty file output (reg.csv) from `pyscenic ctx`,...
Bumps [numpy](https://github.com/numpy/numpy) from 1.20.1 to 1.22.0. Release notes Sourced from numpy's releases. v1.22.0 NumPy 1.22.0 Release Notes NumPy 1.22.0 is a big release featuring the work of 153 contributors spread...
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Bumps [dask](https://github.com/dask/dask) from 2021.2.0 to 2021.10.0. Commits 97494ff bump version to 2021.10.0 ac01ddc da.store to create well-formed HighLevelGraph (#8261) 9f0f002 CI: force nightly pyarrow in the upstream build (#8281) a544670...
Bumps [distributed](https://github.com/dask/distributed) from 2021.2.0 to 2021.10.0. Commits 63ebaea bump version to 2021.10.0 1670cf8 Ensure resumed flight tasks are still fetched (#5426) cdc68cc AMM high level documentation (#5456) 33d83bc Provide stack...
Bumps [pillow](https://github.com/python-pillow/Pillow) from 8.1.1 to 9.0.1. Release notes Sourced from pillow's releases. 9.0.1 https://pillow.readthedocs.io/en/stable/releasenotes/9.0.1.html Changes In show_file, use os.remove to remove temporary images. CVE-2022-24303 #6010 [@radarhere, @hugovk] Restrict builtins within...
**Describe the bug** When I try to install pySCENIC using python version 3.9 the installation drops with an error It works in python 3.8. The error seems to be related...
Hi, Is there an easy way to add NES and p-value/q-value and other filters to the auc_mtx or keep as separated files ? If so, we can filter the regulons...
**Describe the bug** When running pyscenic grn from a singularity container, a segmentation fault is raised. However, the output data is successfully generated. This bug has been reported before but...
Hello, As I have understood, Pyscenic uses dask for multiprocessing which is great. How about GPU capabilities? I don't see pyscenic using GPU and am wondering if GRNBoost2 algorithm can...
**Describe the bug** when running command below I get **NameError: name 'gene_names' is not defined** error https://github.com/aertslab/pySCENIC/blob/master/src/pyscenic/cli/arboreto_with_multiprocessing.py following this script, my data is expression matrix with row=cellid, column=genes **Steps to...
