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For the following pyHiM output, it might be nice to know which RT correspond to which color
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Paper: https://www.nature.com/articles/s41592-023-01938-4
Abstract:
Joint profiling of chromatin accessibility and gene expression in individual cells provides an opportunity to decipher enhancer-d…
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An example to run a gene-cluster simulation without actin is:
python run_single_shoebox.py -b 11 -r 1 -t 10 -o gene_cluster/ -m 1 -c Control -p 3 -a 30 -x 80 -z 0 -n 0.01
where:
- a: activation…
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Hi!
How easy/seamless is it to add community contributed plugin track? Are there any examples/demonstrations available?
Thanks,
Parul
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There is no reason to annotate to this directly. You always know the mechanism based on the species
There are 25 direct experimental annotations that could be auto pushed down https://amigo.geneonto…
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### Data Owner Name
ALLEN INSTITUTE/Chan Zuckerberg Initiative/GeoNet
### Data Owner Country/Region
United States
### Data Owner Industry
Life Science / Healthcare
### Website
https://www.allen…
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With chain configuration files we can specify if a chan is inhibited or permissible to transcriptional activation.
We would like to be able to specify the inhibition flag also at the single-cell leve…
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Hello,
I am encountering an issue with preprocess. During generation of TF binding, I get an error
```
preprocess(TG_pseudobulk,RE_pseudobulk,GRNdir,genome,method,outdir)
Mapping gene exp…
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Hi, I am tring to call peaks using macs2 from ATAC-seq data.
many papers use --shift -100 --extsize 200 for MACS2 rather than -f BAMPE; but my data is paired_end reads，if I use -f BAMPE, then the …