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Hello,
I am currently attempting to identify the denovo motifs enriched in a different mouse strain using the denovo_motifs function but keep receiving the following errors:
Loading shift vector…
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### Purpose
Originally, the task of this issue was to use pattern4 as the tool to analyze the class files of a project via generating a xml. Then, afterwards, generating a table from the provided xml…
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Hi,
I am interested to your amazing work presented in ICML 2024.
but when I look into the github, I cannot find any of pre-defined motif txt files.
Is there any way to generate or get the p…
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Hello!
I'm using modkit for a bacterial (epi)genomics project. I have a large, GC-rich bacterial genome with several methyltransferases which may or may not be expressed under culture conditions. …
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Thank you for developing this fantastic tool for visualizing HOMER results! I truly appreciate your efforts in making data visualization more accessible.
I have a question about using the heatmap f…
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Hello,
I wanted to report this error when running `motif discovery`.
```
Traceback (most recent call last):
File "/Accounts/gkanaan/miniconda3/nanomotif/bin/nanomotif", line 8, in
sys.…
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When grouping motifs into communities (`vame.community()`), depending on the value of `cut_tree`, some motifs are left out and not grouped in any of the created groups. Changing `cut_tree` to lower va…
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Hi team,
It was seeing your poster at ISME. I wanted to follow up on my question with an issue to serve as a (hopefully useful) reminder. It would be cool to benchmark your motif finding with `modk…
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Dear team,
Is there an error in the motifs included in the STR pathogen bed file?
For example, for the DAB1 gene, you have indicated the following motifs:
![image](https://github.com/user-attachmen…