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Hi, I have a short question concerning the Arima kit:
according to https://nf-co.re/hic/docs/usage the following is stated:
--restriction_site
ARIMA kit: ^GATC,^GANT
--ligation_site '[Ligation m…
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Hi @tanlongzhi,
Hope you are doing good!
I have read the definition of single-cell chromatin Compartment in your paper, which is that
> the single-cell chromatin compartment for each 1-Mb bin …
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Hi there,
I wonder if you can provide a small example in the current repo to run your program ?
To be precise, I am unsure of the formatting of labels & chromatin_tracks
```
train:
seq:…
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In the past, Jung et al. 2019 replaced Javierre et al. 2016. We want to keep both datasets. @MayaGhoussaini commented on this:
> We integrated Jung et al in 2019 after Takeda pointed it. It looks a…
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Hi, Thanks for this tool. I have been playing around with the tutorial with a set of paired scRNA/ATAC data but still having some trouble inferring GRN so was hoping to get some input.
This may be …
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Hi, Dr. Zhu, I'm processing ATAC data of Paired-seq using Signac
```
counts
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Dear Dr.Karbalayghareh,
Hope all is well!
I'm interested in your paper Chromatin interaction–aware gene regulatory
modeling with graph attention networks, especially on Figure 3. …
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Hi,
Is there a set of p-values associated with the NITE scores for genes and cells in your RP model? I am trying to find a quantitative metric to decide whether a set of genes I am interested in ar…
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Please provide as much information as you can:
* **Suggested term label:**
- histone loading activity
- histone unloading activity
* **Definition (free text)**
histone loading activity …
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Dear authors,
Thanks for building these tools. I would like to ask about the footprint analysis: is there a quantification metric for the footprint inferred by hint-atac? With the default, the outp…