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, First, I would like to thanks for the great package and nice tutorial. **Describe the bug** I followed the protocol of [PBMC10k](http://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.html). Everything went smooth before the pyscenic step....
hey, i have got file in h5ad format and i wanted to convert it to .h5seurat format so that i can read in R I used the following code: Convert("D:/Seema/seema/endothelial...
Dear pySCENIC developer team, First of all, thanks for the excellent work. I am running into a conceptual issue that I cannot find a solution for. I have been trying...
Hello pyscenic, For the heatmap (coding below), is it possible to sort it by cell type colors? I mean the cells from the same cell types aggregate together to make...
A recurring problem is that the GRN inference step of pySCENIC (using [Arboreto](https://github.com/tmoerman/arboreto)'s GRNBoost2/GENIE3 implementation) fails to complete successfully. This seems to be due to issues with newer Dask releases...
I have a few TFs that appear to be missing from the TF list seen in this file: hs_hgnc_tfs.txt, which is available in the resources folder. The TFs are: ZFHX4...
Hi! I added the possibility that users can freely choose the cutoff for `module2df` in the `ctx` step of pySCENIC. I had the issue that [this error](https://github.com/aertslab/pySCENIC/blob/2919ae49d124ddceb8a1c296b2d1d37c3e851325/src/pyscenic/transform.py#L244-L248) was triggered for...
Hi, I am new to bioinformatics and pySCENIC. I am trying to analyze my targeted single-cell RNAseq dataset with 428 genes but got an error at the first step. Below...
Dear SCENIC team, Thanks for the great tool SCENIC! I have encountered an error when i try to analyze my 10X genomics scRNAseq data followed the instruction "https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.ipynb". I just...
my code: df = prune2df(rnkdbs=dbs, modules, MOTIF_ANNOTATIONS_FNAME) The error is: ValueError: The columns in the computed data do not match the columns in the provided metadata Extra: [] Missing: []...
