User: Collin

gravatar for Collin
Collin830
Reputation:
830
Status:
Trusted
Location:
United States
Last seen:
8 hours ago
Joined:
4 years, 8 months ago
Email:
c************@gmail.com

Posts by Collin

<prev • 95 results • page 1 of 10 • next >
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Comment: C: Get clinVar info for SNP with VEP
... My experience is similar in that disk speed can limit the speed of annotation. If you have a machine with a SSD you'll definitely get a speed boost. See the wiki for more detail: https://github.com/KarchinLab/open-cravat/wiki#system-capabilities . ...
written 6 weeks ago by Collin830
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Comment: C: Get clinVar info for SNP with VEP
... At least in my hands your first variant is generating a synonymous variant (BRAF D638D), which is not the same thing as the listed pathogenic variant. ...
written 6 weeks ago by Collin830
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Answer: C: Get clinVar info for SNP with VEP
... A lot of variants will likely produce an empty ClinVar field because ClinVar pathogenicity assertions are only available for a small number of variants. However, you could cross reference annotations with another variant annotator just to be sure. For example in [OpenCRAVAT][1], you could submit dir ...
written 6 weeks ago by Collin830
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Comment: C: Variant effect prediction
... A little clarification might help. Are you trying to predict whether variants are functionally damaging to proteins or are pathogenic (i.e. disease related)? Also, you mention a genome, are you also trying to prioritize non-coding variants? ...
written 8 weeks ago by Collin830
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Comment: C: How to go from VCF file to protein level
... Another potential alternative is [OpenCravat][1] [1]: https://opencravat.org/ ...
written 8 weeks ago by Collin830
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Comment: C: Mutation clustering in protein domains
... A word of caution about visual confirmation is that mutations can preferentially occur at certain nucleotide sequence contexts (e.g. CpG) which are not necessarily evenly distributed across the CDS of a protein. ...
written 3 months ago by Collin830
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Comment: C: How to download passenger mutations for cancer
... In CHASMplus, I used somatic mutations calls from the TCGA MC3 effort (pmid: 29596782), which provided a completely standardized way of mutation calling. Their pipeline was automated, so there likely are incorrect variant calls, but at least the data is consistent across many tumors. Another "gotch ...
written 3 months ago by Collin830
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Comment: C: How to download passenger mutations for cancer
... There are only one to several driver mutations per tumor, so the task of identifying driver mutations is your classical "needle in the haystack" problem. In my case, since I was using random forest, the under sampling was done through the bagging procedure of the random forest (randomForest R packag ...
written 3 months ago by Collin830
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Answer: A: How to download passenger mutations for cancer
... You'll fist need to clarify what exactly you mean by driver mutation vs passenger mutation. 1) Are you concerned with somatic mutations or germline mutations (most often it is somatic, if you say "driver mutation")? 2) Are you concerned mostly about protein-coding mutations or non-coding mutations? ...
written 3 months ago by Collin830
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Answer: A: Getting a list of tumor suppressors
... One source is the Cancer Gene Census (https://cancer.sanger.ac.uk/census ), which provides a list of cancer driver genes and has labels for both oncogenes and tumor suppressor genes. If you are interested in one of the many cancer types available from The Cancer Genome Atlas, the driver gene analysi ...
written 4 months ago by Collin830

Latest awards to Collin

Appreciated 25 days ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Scholar 3 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 4 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Scholar 4 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Appreciated 19 months ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 2.3 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 2.4 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Supporter 2.4 years ago, voted at least 25 times.
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 3.7 years ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 3.7 years ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 4.2 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 4.2 years ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 4.3 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 4.3 years ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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