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### Description of feature
Store genes that are filtered out somewhere in the pipeline. These could be useful for development and may be of interest in certain research contexts
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### Exploit Reports
- [x] I confirm this issue is not an exploit. (Required)
### BYOND Version
515.1642
### Issue Description
A monkey had horns despite not having any SE gene above 801
### What…
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Hi,
I am using the egapx-0.3 to annotate an insect genome, i find some genes exon structure seems not right. Do you know how to improve this?
![test](https://github.com/user-attachments/assets/106…
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I have read in your documentation that
**_The new.prism function removes any genes in the mixture greater than 1% in more than 10% of the mixture samples by default. This threshold is very lenient…
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three letters from genus
four letters from species
example : For Phytophthora sojae, gene prefix will be Physoja instead of Physo
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Hi, thanks for your great work to develop so excellent method! I wonder if I could apply sylph for profiling functional genes, like ARGs and KO (from KEGG)?
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This is because the human gene has a preferred label of `tp53`, while the mouse gene has a preferred label of `trp53`. It is therefore being sorted below all the other genes that have a preferred labe…
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When using the pre-trained weight from SCimilarity, how does `VAE_train.py` account for different genes between user provided adata and SCimilarity? What if a gene is present in user's data but not in…
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Hello,
I got the TSSs from the gtf file, and some genes have multiple TSSs (this happens for genes with a "trans-splicing" label). My gene expression matrix only has one row (entry) per gene. What…
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### Report
```
!lamin init --storage ./run-tests --name run-tests --schema bionty
import lamindb as ln
import bionty as bt
adata = ln.core.datasets.anndata_pbmc68k_reduced()
curator = ln.C…