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...
Good afternoon! Is it possible to obtain somehow genome coordinates for human motif annotation database ([HGNC annotation](https://resources.aertslab.org/cistarget/motif2tf/motifs-v9-nr.hgnc-m0.001-o0.0.tbl))? I saw #83 but actually I just want to filter some rows from...
Hi, Does PySCENIC have anything similar to plotTsne_AUCellApp function in R version? if not, is there any option to transfer PySCENIC results (say, auc matrix and regulons) to R SCENIC...
Hi guys, really liking the pySCENIC adaptation (saving alot of time in our hands!) however, Im having the following issues with pySCENIC grnboost (through command line) when running on a...
Hi, I am unable to run pySCENIC on ubuntu 16.04 LTS edition, 64 bit. I have created a conda environment called `pysenic` using below command `conda create -n pysenic python=3.6`...
Using the pySCENIC 0.9.4 CLI, I get the following error on the ctx step. This seems to be related to the most recent version of dask (v1.1.0), since when I...
Hi, I have been trying to use the loom file generated by pySCENIC on ScopeLoomR to further manipulate it. The loom file generated by pySCENIC from a windows platform has...
My package version list: > arboreto 0.1.5 > dask 1.0.0 > distributed 1.25.1 > pyscenic 0.8.16 When I ran the code in the demo: ``` import os import glob import...
Dear pySCENIC developer, Thank you for your excellent work. This is Mengfei Wang from Dalian Medical University. When I tried to run grn, there were some error messages about tornado.application....
**Describe the bug** After running the arboreto function it is not clearing the memory. using 64 cores with 900 gig memory and after finishing it keeps using 600gig for some...
Hi, I am running pyscenic ctx and it worked. ``` pyscenic ctx adj.csv ../related_info/cisTarget_Ath/Athaliana.genes_vs_motifs.rankings.feather --annotations_fname ../related_info/cisTarget_Ath/JASPAR_plantTFDB_Ath.tbl --expression_mtx_fname result/processed_result/CIM1d_rep2.loom --mask_dropouts --num_workers 40 --output reg.csv ``` But I have a question about...
