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...
**Describe the bug** pyscenic -h errors out after fresh installation via conda. Seems numpy new version does not include np.object. Only object is there: Following steps of installation on anaconda3...
Thanks a lot urget help needed **Describe the bug** A clear and concise description of what the bug is. > Mote that most *errors* are due to the input from...
Hello pyscenic team, I am experiencing an error while running pyscenic ctx: 'pandas.errors.ParserError: Could not construct index. Requested to use 2 number of columns, but 3 left to parse.' The...
auc bug
Hi, I have used the CLI version of pyscenic. Everything appears to have run successfully but then I get this error with this code: import json import zlib import base64...
For **questions** about using SCENIC, please use the Discussions: https://github.com/aertslab/SCENIC/discussions/ Create an issue only to report **bugs**. > Mote that most *errors* are due to the input from the user,...
I used pyscenic ctx in CLI and my output has AUC values (third column) What does this mean exactly? I only have values below 0.4. This means that all regulon...
Hello, When using pySCENIC for transcription factor activity analysis, I encounter the following transcription factor names, such as, E2F8(+) E2F1(+) MYBL1(+) MYBL1(-). How should I interpret these results? What do...
The transcription factor (TF) gene symbols in the recommended list to be used with pySCENIC (https://resources.aertslab.org/cistarget/tf_lists/allTFs_hg38.txt) include some genes that are assessed to not be TFs based on Lambert et...
This PR pins numpy to avoid issues on fresh installations as described in #477 . If you had this already on some other branch waiting to be merged, feel free...
From the SCENIC paper: "Only modules with significant motif enrichment of the correct upstream regulator are retained, and pruned to remove indirect target genes without motif support." Does the --no_pruning...
