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...
**TypeError: Must supply at least one delayed object** Input matrix >>> ex_matrix = pd.read_csv(SC_EXP_FNAME, sep='\t', header=0, index_col=0).T >>> ex_matrix.head() GENE Mrpl15 Lypla1 Gm37988 Tcea1 Atp6v1h Rb1cc1 4732440D04Rik Pcmtd1 Gm26901 Rrs1...
Hello, I am currently learning how to use pySCENIC, and ran the given tutorial. Right before the last step of the pySCENIC pipeline of creating the AUC matrix, it is...
**Describe the bug** If I following the install procedure through `conda create -n scenic_protocol python=3.6`, I can only install pyscenic=0.11.2. Under python 3.6, I could not upgrade ctxcore to 2.0.0...
I am comparing different conditions. running them separately using pyscenic using the same seed. I aggregated the different runs. A target has high occurrence (10/10 times it appeared) for a...
**Description** I'm running the tutorial and I keep getting the errors at the `prune2df` step like this: ```pytb Exception: 'KeyError(\'Field "Snora5c" exists 2 times in schema\')' [...] Exception: 'KeyError(\'Field "1600002H07Rik"...
https://github.com/aertslab/pySCENIC/blob/06bafba412792f6efa5a552a23bb221cc3bdea1b/src/pyscenic/export.py#L279 The `export.py` of `binarize` function did not include the `seed` parameter. It would be helpful to add it so that the results can be fully reproduced.
Hi, I’m quite new to this type of analysis, and I’m encountering some issues while running the SCENIC pipeline on two single-cell RNA-seq datasets from closely related butterfly species. I...
**Describe the bug** I [just fixed the bioconda recipe for `pyscenic`](https://github.com/bioconda/bioconda-recipes/pull/60625), including adding upstream packages to `conda-forge` and fixing the `ctxcore` recipe as well. It now installs and at least...
Hi, thank you for this wonderful package. I have two questions for its application. (1) I run the whole process without any errors in my python, only many warnings like...
