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The paper ["Integration of Biomass Formulations of Genome-Scale Metabolic Models with Experimental Data Reveals Universally Essential Cofactors in Prokaryotes"](https://pubmed.ncbi.nlm.nih.gov/2793957…
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Potentially related to: https://github.com/kaizhang/SnapATAC2/issues/360.
A few folks at the Allen Institute have now noticed the normalized bigwigs from snapatac2 don't follow our expectations of …
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This feature aims to enhance the current genome encoding model by integrating an **autoencoder** to compress and encode neural network weights into a latent vector. The autoencoder will replace the di…
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as described in -
Genomes on a Tree (GoaT): A versatile, scalable search engine for genomic and sequencing project metadata across the eukaryotic tree of life. Challis et al. 2023. Wellcome Open R…
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**CHM13V2 T2T Assembly**
```bash
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.fna.gz
snipe sketch --ref GCF_00…
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I have some troubles with TSSlogo. I load the annotation from txdb like this:
```
tx_annotation_obj -> .TSSlogo -> getBSgenome
```
for checking:
```
> x subset(annotation == "promoter")
> …
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```
### Pipeline run code and environment:
* Command: `/my/path/pepatac/pipelines/pepatac.py -O /my/path/OUTPUT -P 10 --sample-name sample_S1_R1_001 --input /my/path/FastQ/sample_S1_…
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Hi!
I'm running the new OrthoFinder3 on two species sets - Species51 and Species67. Species in both represent animal phyla or their major unicellular outgroups. Phylogenetically, it is structured a…
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Can I use GALBA for predicting the genes of a gene family?
Suppose, for example, that I'm interested in finding all cytochrome P450s in a particular species. It would be very nice to be able to giv…
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- [ ] Editor should be able to handle giant sequence loaded
- [ ] onSave hook should have option to just save the changes