User: brett.spurrier

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Posts by brett.spurrier

<prev • 9 results • page 1 of 1 • next >
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Comment: C: How to download a full matrix of gene expression of a TCGA dataset
... There doesn't seem to be a "download button" anymore as you mentioned. Nor does the link work - but this is 3yrs old, so I'm not surprised. ...
written 3 months ago by brett.spurrier20
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Comment: C: Using VEP to get gnomAD frequencies
... This is a big help in understanding whats going on. Thank you. Would you recommend converting the VCF to have (+) strand alleles only? As a side note, this VCF is directly downloaded from cosmic, so I suppose it makes sense that the "ref" alleles might be super rare. ...
written 9 months ago by brett.spurrier20
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Comment: C: Using VEP to get gnomAD frequencies
... I did notice that as well. So why would VEP be returning anything then? Seems odd (again). There are other entries with a `-` in place of the AF (I'm assuming that means no data). ...
written 9 months ago by brett.spurrier20
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Comment: C: Using VEP to get gnomAD frequencies
... Answered my own question by looking at more data. Nope, there are plenty of `+1` strand entries with the same frequency issue as the first example. ...
written 9 months ago by brett.spurrier20
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Comment: C: Using VEP to get gnomAD frequencies
... Interesting. Could that be because the strand is `-1`? ...
written 9 months ago by brett.spurrier20
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Using VEP to get gnomAD frequencies
... Hi all, I am using Ensembl VEP (command line) to annotate a VCF I have. I am specifically looking for gnomAD allele frequencies, which is fairly straight forward to do, technically speaking. However, the data looks off in some cases. For example, when I pass in: 10 69408929 COSM3751912 A T . ...
annotation frequency vep gnomad allele frequency written 9 months ago by brett.spurrier20 • updated 9 months ago by Emily_Ensembl19k
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Answer: A: How can I align a generated ligand (from SMILES) to a ligand in a PDB?
... I think I hav found an answer using OpenBabel. obfit "Oc1ccc(cc1O)C1Nc2cccc3cccc(N1)c23" fixed.pdb moving.pdb > new_aligned.pdb Where the smiles pattern matches my moving.pdb (which is where my generated conformers came from). ...
written 2.5 years ago by brett.spurrier20
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Comment: C: Ligand alignment to a fragment of a protein structure
... This looks like it might work if the number of atoms is the same between the two molecules, and the original post said this is **not** the case. In other words, `ref_atoms` and `samples_atoms` needs to be identical in length. Am I wrong here? ...
written 2.5 years ago by brett.spurrier20
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How can I align a generated ligand (from SMILES) to a ligand in a PDB?
... I have a ligand that exists in its own PDB (*reference PDB*). I have then generated another (structurally similar, but not exact) ligand from SMILES, and written that to a PDB. I am trying to find out how to superimpose the generated ligand onto the reference PDB, but I am having trouble finding a ...
pdb assembly superimpose ligands rdkit written 2.5 years ago by brett.spurrier20

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Scholar 2.5 years ago, created an answer that has been accepted. For A: How can I align a generated ligand (from SMILES) to a ligand in a PDB?

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