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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/rhielab/TENET.AnnotationHub
Confirm the following…
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Hello,
I would like to know how MultiVI associates ATACseq peaks to genes. Does it associate it to TSS up/down some specific distance, or does it associate it to to the full gene including intr…
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### Search before asking
- [X] I have searched the YOLOv8 [issues](https://github.com/ultralytics/ultralytics/issues) and [discussions](https://github.com/ultralytics/ultralytics/discussions) and fou…
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### Description of the bug
Hi, Dr Ou.
I am using your hicar pipeline. I download the test data, but I do not find the MAPSpeak dir in result file. I am wondering whether you can give me some advice.…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/rhielab/TENET3.data
Confirm the following by edit…
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**Problem**: `FindMotifs` gives a (slightly cryptic) error message when run with only one feature
```r
library("Signac")
library("JASPAR2020")
library("TFBSTools")
library("BSge…
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Hi,
I found that there are cases where regions overlap. For instance the first line below overlaps with the 3 subsequent regions.
```
chr1 146261547 148712700 40_EnhWk6
chr1 1468…
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Are the default options from [bedtools merge](https://bedtools.readthedocs.io/en/latest/content/tools/merge.html) good enough for this use case, or are there other methods we should consider?
@kopa…
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Hello! I am a developer in the MACS3 project, and we are using `hmmlearn` to build an HMM for detecting open chromatin regions from ATAC-seq data. Without the PR #545, we can't reproduce our results f…
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Hi,
I saw previous issues mentioning this, but also saw that the change to FoldChange() was implemented in v1.3.0. I am currently using Signac v1.4.0. I'm not sure if the change is working as inten…