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With our current implementation the scores for PPI hits to direct StringDB interactors don't end up much above those to quite distant interactors in the network. This is not clear without manual inves…
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Here, I report the heatmap for Top similarity and top anti-similarity pairs without known evidence behind it.
Procedure:
1. Select top 20 similar pairs according to ORF profiles cosine similarity …
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I have install the Divine tool (https://github.com/hwanglab/divine/blob/master/documents/tutorial/divine_tutorial.md) but when I run the following command, I have got the error as shown below.
$ divi…
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From uniprot.org, will be to initialize node vectors of our graph neural network.
Information Needed
- Source of data
- Where data is located
- Description of data
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I loaded a fasta file containing 4542 sequences with average length of 2.5kb, however only 4539 sequences were in the pyfastx.Fasta object.
```
fa = pyfastx.Fasta('assembly.fasta')
fa['contig_4540'…
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Suggestions:
- [x] C. elegans
- [ ] E. coli
- [x] S. cerevisiae
- [ ] Plant species: http://zzdlab.com/plappisite/index.php
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On NodeNorm, [ENSEMBL:ENSP00000263368](https://nodenormalization-sri.renci.org/1.3/get_normalized_nodes?curie=ENSEMBL%3AENSP00000263368&conflate=true) exists as a single-identifier clique. However, ve…
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Here is the updated list they provided Dec 15 2023.
We are generally interested to find gene pairs where:
- there is a strong Cell Painting ORF pos or neg correlation (column E: ORF_similarity_ab…