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Hi,
I am going through the vignette on Analyzing PBMC scATAC-seq. I run the following line and get this error:
> pbmc head(Annotation(pbmc))
GRanges object with 6 ranges and 5 metadata columns…
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Hi developers,
I hope this message finds you well. I have a quick question about the UCSCXenaShiny app in R. Is it possible to use human chromosome coordinates, like chr1:68044026-68054909, as a qu…
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Hi,
I have the following cases that have fusions confirmed by FISH and RT-PCR. However these fusions cannot be picked up by Arriba, not even in the discarded list. However, these fusion can be call…
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Hi,
I was wondering how to plot a GeneHancer track (.bed file) in pygenometracks that looks like the one in UCSC browser(Promoters in red scale and Enhancers in grey scale)
![Screen Shot 2023-08-1…
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Check and add exp annotation for examples:
- [x] chromatin-protein adaptor activity (GO:0140463)
XIST URS000075D95B_9606
Epigenetic silencing via interaction with X chromosome to recruit chro…
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First of all, thank you for making this amazing package to help mitigate multiome data analysis. It is of humongous help.
I was wondering how to generate the coverage plots with the peak accessibilit…
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Hello,
The DeepSTARR looks a great tool to predict enhancer activity from DNA sequences.
Would you like to tell me whether DeepSTARR can predict the motif from gene promoters? I also want to…
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NOTE: the KW-0418 mapping and individual genes below are just examples to demonstrate a wider problem.
* **UniProt KeyWord (ID and label):**
Kinase KW-0418
* **Sequences with problematic anno…
sjm41 updated
10 months ago
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Hello,
thanks for creating this useful tool :)
When I run through the pipeline, I get stuck with the following error (command and error shown):
```
python "$abc_path"run.neighborhoods.py \
--cand…
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**Describe the bug**
Hello,
The errors below occurred with the following input. They consistently showed up whether I used n_cpu of 1, 6, or 10.
**To Reproduce**
```
from scenicplus.wrap…