User: Collin

gravatar for Collin
Collin470
Reputation:
470
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Trusted
Location:
United States
Last seen:
15 hours ago
Joined:
2 years, 2 months ago
Email:
c************@gmail.com

Posts by Collin

<prev • 60 results • page 1 of 6 • next >
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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 29 days ago by Collin470
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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 4 weeks ago by Collin470
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Comment: C: 2020+ installation problems:
... What python version and operating system are you using? ...
written 4 weeks ago by Collin470
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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 4 weeks ago by Collin470
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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 7 weeks ago by Collin470
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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 7 weeks ago by Collin470
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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 7 weeks ago by Collin470
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Comment: C: pathogenicity predictors of cancer mutations
... I've personally aggregated a set of 8 benchmarks for missense mutations comprising in vitro experiments, in vivo experiments, and literature curated databases (OncoKB). CADD and MCAP didn't perform as well. ...
written 7 weeks ago by Collin470
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Comment: C: pathogenicity predictors of cancer mutations
... The top 4 I would recommend for missense mutations would be CHASM, CanDrA (version "plus", with "cancer-in-general"), FATHMM cancer, or ParsSNP. From examining prior benchmarks and my own benchmarks, these seem to perform better. Some methods which are designed for germline mutations are decent (eg. ...
written 7 weeks ago by Collin470
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Comment: C: pathogenicity predictors of cancer mutations
... Are you interested in somatic mutations or germline mutations? The answer depends on your intended use. ...
written 7 weeks ago by Collin470

Latest awards to Collin

Appreciated 4 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 14 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 14 months ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 21 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 22 months ago, asked a question with at least 3 up-votes. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Scholar 22 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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