User: Collin

gravatar for Collin
Collin700
Reputation:
700
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United States
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10 hours ago
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4 years, 3 months ago
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Posts by Collin

<prev • 83 results • page 3 of 9 • next >
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Comment: C: Alternative tools replace MutDB to predict consequences of deleterious SNV
... Could you clarify whether you are interested in germline mutations or somatic mutations? The table you include has many cancer-specific methods, but the semantic "deleterious SNV" would suggest you are interested in germline mutations. ...
written 2.0 years ago by Collin700
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Answer: A: Alternative tools replace MutDB to predict consequences of deleterious SNV
... You could use scores from the VEST algorithm (PMID: 23819870). It's pretty easy to score SNVs by just submitting them to the CRAVAT webserver (http://www.cravat.us/CRAVAT/, PMID: 29092935). In one of the latest papers to benchmark performance, VEST is among the best (PMID: 29179779). ...
written 2.0 years ago by Collin700
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Comment: C: Why GWASs cannot speculate what kind of mutation the SNP would cause?
... My assumption is that generally the "lead" SNPs identified as most significant in GWAS are not necessarily the actual causal SNP because of linkage disequilibrium. Therefore trying to ascertain a function or effect of those SNPs would be misleading. I believe they generally try to do further studie ...
written 2.0 years ago by Collin700
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Comment: C: 2020+ installation problems:
... The simulations are mostly useful for 20/20+. What are you intending to do that isn't already done in the pipeline for 20/20+ (2020plus.readthedocs.io/en/latest/ )? ...
written 2.2 years ago by Collin700
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Comment: C: 2020+ installation problems:
... Are you missing any of the following files: genes.fa, genes.bed, or mutations.txt (FASTA, BED, or mutation file)? The instructions on the probabilistic2020 web site (http://probabilistic2020.readthedocs.io/en/latest/tutorial.html ) are meant for three hypothetical files, and actually need to be pro ...
written 2.2 years ago by Collin700
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Comment: C: 2020+ installation problems:
... What python version and operating system are you using? ...
written 2.2 years ago by Collin700
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Comment: C: Calculating direction of beta stand
... I believe the direction is just going from the N-terminus to C-terminus of the protein. It's helpful when interpreting different beta sheet motifs. ...
written 2.2 years ago by Collin700
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Comment: C: pathogenicity predictors of cancer mutations
... I tweaked the wording of my reply so it is less ambiguous. I was actually talking about the approach Kevin suggested by analyzing protein conformation changes when the actual amino acid is substituted in the protein structure. I actually know Eduard personally (the first author on the papers you lin ...
written 2.2 years ago by Collin700
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Comment: C: pathogenicity predictors of cancer mutations
... It does the best that I've seen for methods not tailored to cancer/somatic mutations. I'd recommend to stick with the cancer specific predictors unless you need to assess some other type of alteration that is not missense. ...
written 2.2 years ago by Collin700
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Comment: C: pathogenicity predictors of cancer mutations
... Do you know if there is a paper that assesses the performance of this approach on somatic mutations? Analyzing mutational clustering in protein structures has shown to perform well, but I'm not aware of successful methods taking a pure biophysical/protein conformation approach for cancer. ...
written 2.2 years ago by Collin700

Latest awards to Collin

Appreciated 14 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 16 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 23 months ago, created a question with more than 1,000 views. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 2.0 years ago, voted at least 25 times.
Appreciated 2.4 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 3.3 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 3.9 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 3.9 years ago, asked a question with at least 3 up-votes. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Scholar 3.9 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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