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Hi everyone. Great work for the new paper. I'm trying to replicate the results in your joint ATAC-seq and RNA-seq paper. I saw that for the analysis of A549 ATAC-seq, you mention that the procedure wa…
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I am working on ATAC-seq mice data and have developed a function to run bias model training across all folds and comparison groups. While testing the function with fold 1 and the group fed_vs_fasted_0…
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Hi @martinkim0 and all
Similarly to https://github.com/scverse/scvi-tools/pull/2249 by @lauradmartens would be great to have a MultiVI version with Poisson or even NB likelihood for ATAC data. How …
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Hello,
I'm currently exploring [ATAC](https://github.com/Julien-cpsn/ATAC) as a potential replacement for `curl`.
However, for cybersecurity purposes, I frequently use curl with the `--path-as-i…
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```
$ diff topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.ga topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.ga
$
```
@heylf do you have an idea which should be d…
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Hi,
when I tried to run caper with encode-atac-pipeline, I could see the job was submitted to the lsf system, but the job disappear immediately without any reports.
when I looked into the detai…
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Hi! I ran into this error:
“Error in checkGrep(grep(".A.txt", files)) :
Improper folder specification; file missing / extra file present. See documentation
Calls: importMito -> checkGrep
E…
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Hi,
Thank you for the amazing model!
I was wondering if there is any guidance for how to fine-tuning the model? I would like to finetune the model with my human data in both atac- and rna- sequ…
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Currently, many new analytical needs have emerged in single-cell ATAC-seq. Why doesn't ArchR consider accommodating them?
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