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Recent Replies
Comment: Distribution of assayed SNPs per sample
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am29
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The vcf file looks like this:
CHR BP SNP ID GENOTYPE SAMPLE ID
1 5234 1:5234 ./. SAMPLE_1
Comment: Distribution of assayed SNPs per sample
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I am interested in whether the reason might not be that individuals are genotyped with different SNP chips but that genotype calls for geno…
Comment: How do I change the title font size in ViolinPlot (Seurat)
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wow this ampersand hack is crazy, thank you! I've been in the R field since 2015 and didn't know this thing
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Did you see this announcement:
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For modeling, check out the [AlphaFold Server][1] for predicting protein structure.
[1]: https://alphafoldserver.com/
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Have you read the [wikicrow entry][1] on the gene? Wikicrow is an LLM generated jumping off point, so while you should treat the informatio…
Answer: Map genome positions onto protein coordinates?
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You can use [ensemble VEP][1] to get the protein coding changes.
You can then use [the Genomics 2 Proteins portal][2] to map these changes…
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Yes, check out [the Genomics 2 Proteins portal.][1] The tool allow you to map any feature, including domains onto a protein structure and c…
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Yes, check out [the Genomics 2 Proteins portal][1]. The tool allow you to map any feature, including domains onto a protein structure and c…
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For more intensive analysis, you can consider MD simulations of the mutant protein where you relax the structure after mutation using tools…
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[UniProt][1] will show the secondary structure for areas of the protein with available SIFTS secondary structures (from PDBs). If there is …
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A few databases that have protein structural features are [UniProt][1], [the RCSB PDB][2], and [the G2P portal][3]
Structural features fro…
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There is a tradeoff between speed and information for a mutation:
(1) Fast, visual: tools like MutationMapper[enter link description here]…
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For a quick visual analysis of how a mutation relates to or features in 3D, the [Genomics 2 Proteins portal][1] is designed for this purpos…
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You can start by visualizing protein structures in a variety of different tools, including offline tools like PyMOL (has an online version …
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