User: Collin

gravatar for Collin
Collin870
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870
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15 hours ago
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5 years, 4 months ago
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Posts by Collin

<prev • 109 results • page 1 of 11 • next >
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Comment: C: VEP is very slow. Fork doesnt seem to work
... Also, as it looks like you are trying to annotate somatic mutations (likely in cancer), OpenCRAVAT has more options for predicting oncogenic mutations in cancer beyond sift. Most recent benchmarks suggests there are many other better methods for cancer (https://genomebiology.biomedcentral.com/articl ...
written 16 hours ago by Collin870
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Comment: C: VEP is very slow. Fork doesnt seem to work
... I'm not a VEP user, but if you can't figure it out then you can always use another variant annotator like [OpenCRAVAT][1]. My experience is that it should only take several seconds to annotate 1000 variants (docs here: https://open-cravat.readthedocs.io/en/latest/ ). [1]: https://opencravat.org/ ...
written 17 hours ago by Collin870
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Answer: A: Is there a tool to predict if a missense variant causes a loss of function on th
... As some one who does a lot of variant interpretation in cancer genomes, a priori it is more likely the variant is loss-of-function than gain-of-function. This is for two reasons: 1) pathogenicity predictors are typically better at predicting pathogenic loss-of-function mutations (you indicated that ...
written 9 weeks ago by Collin870
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Comment: C: Is there a tool to predict if a missense variant causes a loss of function on th
... I don't think the link is relevant for missense mutations as specified by the poster. Missense mutations can be loss-of-function without truncating the protein. ...
written 9 weeks ago by Collin870
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Answer: A: SNP annotation tool
... You could try opencravat (https://opencravat.org/ ), which is available through a website, command line tool, or a local graphical interface. ...
written 3 months ago by Collin870
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Comment: C: TCGA driver mutation data
... Glad to help. Hopefully this can also help anybody else that had the same question as you. ...
written 3 months ago by Collin870
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Comment: C: Protein_Change in MAF
... For additional reference, the description of the HGVS format can be found on their website (https://varnomen.hgvs.org/ ) or in the paper (https://onlinelibrary.wiley.com/doi/full/10.1002/humu.22981 ). There is also python packages to parse the format (https://hgvs.readthedocs.io/en/stable/index.html ...
written 3 months ago by Collin870
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Comment: C: TCGA driver mutation data
... Lastly, if you also want to predict driver missense mutations in new tumor samples outside of the TCGA, you could try CHASMplus (https://pubmed.ncbi.nlm.nih.gov/31202631/ ). The results were highly consistent with our results from the TCGA pancanatlas study, but substantially simplifies the scoring ...
written 3 months ago by Collin870
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Comment: C: TCGA driver mutation data
... Many clinical interpretation guidelines clearly delineate that missense mutation in a known disease gene is not sufficient evidence in of it self to be labeled oncogenic/pathogenic. ...
written 3 months ago by Collin870
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Comment: C: TCGA driver mutation data
... For loss-of-function mutations in tumor suppressors, you might look at the genes annotated as tumor suppressors in Table S1. Most variant annotation databases regard frameshift indels, nonsense mutations, essential splice site, stop loss or start loss mutations as likely oncogenic in tumor suppresso ...
written 3 months ago by Collin870

Latest awards to Collin

Centurion 3 months ago, created 100 posts.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Appreciated 8 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Popular Question 10 months ago, created a question with more than 1,000 views. For Music bmr calcBmr: bmr-groups resulting in unitialized centroid and division by zero
Scholar 11 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 12 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 12 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Appreciated 2.3 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 2.4 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Are there recommended steps if MuSiC reports too many significantly mutated genes
Commentator 3.0 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
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Appreciated 3.5 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 3.5 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 4.3 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 4.3 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 4.9 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 4.9 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 5.0 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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