User: Collin

gravatar for Collin
Collin390
Reputation:
390
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Location:
United States
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10 hours ago
Joined:
1 year, 11 months ago
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Posts by Collin

<prev • 42 results • page 1 of 5 • next >
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Answer: A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
... One option may be to look at the BRCA exchange (http://brcaexchange.org/ ) since it's curated by an expert panel. It's supported by the Global Alliance for Genomics and Health, and is a non-paid database. Although I'm not sure if it meets all of your needed criteria. ...
written 12 days ago by Collin390
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Comment: C: MuSic Tools !!!
... If you are talking about using MuSiC from analyzing significantly mutated genes in cancer, then you should be aware that MuSiC has elevated false positives due to how their statistical model handles mutational heterogeneity (PMIDs: 27911828 (includes a method comparison), 23770567). This is particul ...
written 19 days ago by Collin390 • updated 19 days ago by genomax33k
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Comment: C: Exploring cancer mutation data portals
... Are you solely interested in tools that just visualize/download publicly available data sets? What about resources where you can actually submit your own mutations and annotate, analyze, and visualize? ...
written 4 months ago by Collin390
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Comment: C: Genes responsible for cancers
... Tumorportal will only contain genes that are driven by small somatic mutations. This completely leaves out copy number alterations (although they do show copy number on their visual plots) and fusion genes. The cancer gene census from COSMIC, however, doesn't provide that great of breakdown on what ...
written 4 months ago by Collin390
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Comment: C: Statistical test for finding driver mutations.
... If you have your H1 be P != Pg, then you are assuming a two-sided statistical test. You can still have a H1 be P > Pg, which is a one sided statistical test. A one sided test is used, generally, because you are trying to identify cancer drivers. Cancer driver mutations would be more advantageous ...
written 5 months ago by Collin390
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Answer: A: Statistical test for finding driver mutations.
... I'm curious, are you trying to implement a statistical test your self on actual data? It's better to use an already established method (e.g. 20/20+, MutSigCV, OncodriveFML). If you accurately calculate the background mutation rate, you should see roughly half of the genes on either side of the BMR b ...
written 5 months ago by Collin390
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Comment: C: Nobel Prize in Medicine
... One such example, I believe, is the 1979 nobel prize for the development of computed tomography (CT or CAT scan). ...
written 6 months ago by Collin390
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Comment: C: Convert amino acid and nucleotide coding changes between notation formats
... I don't think it's necessary to use the variant effect predictor. I believe the hgvs python package is the somewhat official code to parse HGVS (http://hgvs.readthedocs.io/ ). ...
written 6 months ago by Collin390
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Comment: C: How to conduct pathway analysis from VCF file?
... Unfortunately, CRAVAT is human only. ...
written 7 months ago by Collin390
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Comment: C: Variant frequency calculation
... One tool that might work is CRAVAT (http://www.cravat.us ). I believe it should show the zygosity of variants and frequency if you submit a VCF file. ...
written 7 months ago by Collin390

Latest awards to Collin

Appreciated 12 days ago, created a post with more than 5 votes. For A: BRCA1 and BRCA2 database's for NGS diagnostics purposes
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: ROC curve for biomarkers
Popular Question 10 months ago, created a question with more than 1,000 views. For CRAVAT: a web tool to annotate and analyze cancer variants
Scholar 17 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Difficulty replicating likelihood ratio test from RNA-seq paper
Student 18 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 18 months ago, created an answer that has been accepted. For A: COSMIC data and rare variant

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