Steven

Problem with GRN plot

16

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...

Issue with loom file export function

5

Hi, I run the following function on my date: from scenicplus.loom import * export_to_loom(scplus_obj, signature_key = 'Gene_based', tree_structure = ('Patient 1', 'SCENIC+'), title = 'Gene based eGRN', nomenclature = "hg38",...

Chromsizes URL

4

Hi, I tried to run: # Get chromosome sizes (for hg38 here) import pyranges as pr import requests import pandas as pd target_url='http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes' chromsizes=pd.read_csv(target_url, sep='\t', header=None) chromsizes.columns=['Chromosome', 'End'] chromsizes['Start']=[0]*chromsizes.shape[0] chromsizes=chromsizes.loc[:,['Chromosome',...

Data base

3

Hi everyone, I just realized that my Snakemake pipeline step 3 isn't starting because of the ranking and score database. It seems that every time I download the ranking and...

Colorscale[QUESTION]

1

Hello, Is there a way to change the color scale? I find it quite challenging to work with the default color:  Can we change it for other color like...