scenicplus
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aertslab
SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.
Hi Seppe, I have an issue with this step: ```python consensus_peaks.to_bed( path = os.path.join(work_dir, 'scATAC/consensus_peak_calling/consensus_regions.bed'), keep=True, compression='infer', chain=False) TypeError Traceback (most recent call last) Cell In[26], line 1 ----> 1...
**Describe the bug** While using the snakemake pipeline to process the example data, I encountered the following error ( I only took the the last section since the call stack...
In the "download_genome_annotations" step, "GRCm39" is the target genome for downstream analyses when tha species is mouse. However, compared with "GRCm39", "GRCm38" (mm10) is much more widely used. Can we...
**Describe the bug** Hello. I seem to be getting an error at the get_search_space step in the scenicplus pipeline with snakemake. Any immediate thoughts about why this could be? Should...
Hello, I have a bit of confusion about the Direct and Extended Predicted TF-to-region-to-gene links. I do not understand why there is a distinction between Direct and Extended, what is...
Hello, It seems that the function to plot the GRN on python doesn't work anymore since the recent updates: from scenicplus.networks import create_nx_tables, create_nx_graph, plot_networkx, export_to_cytoscape G, pos, edge_tables, node_tables...
Hello Dear author, In SCENIC+ Tutorial: SCENIC+ step-by-step in the human cerebellum tutorial, there is a file "GRCh38_STAR_2.7.5_rna/genes.gtf" I do not know how to get, may I ask where to...
**Describe the bug** When trying to run "run_pycistarget" I get this error: `ValueError: invalid literal for int() with base 10: '1.17e+08'` **To Reproduce** I was following the 10x multiome tutorial,...
It seems that the development branch had been merged into the main branch two months in the commit 660ea, but the [install docs](https://scenicplus.readthedocs.io/en/latest/install.html) does not udpated yet. 