Moderator: Sean Davis

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Sean Davis22k
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National Institutes of Health, Bethesda, MD
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http://watson.nci.nih....
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seandavis12
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Posts by Sean Davis

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Answer: A: somatic variant calling with no germline sample
... If your goal is to discover new somatic variants, I am afraid that might be quite challenging because the VAST majority of variants in any sample will actually be polymorphisms and not somatic variants. Use of a set of databases of "normal" variation to remove as many germline variants as possible ...
written 9 days ago by Sean Davis22k
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News: Bioconductor 2017 Conference, Boston, July 26-28
... Join us for our annual conference! Dates: July 26 (Developer Day) - 28 Location: Dana-Farber Cancer Institute, Boston, MA, USA Registration: now open. Scholarships available. More information: https://bioconductor.org/BioC2017 The main conference (27 - 28 July) consists of morning scientific talks ...
R bioconductor conference news written 9 days ago by Sean Davis22k
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Comment: C: 2017 NIH SUMMER INTERNSHIP PROGRAM IN BIOMEDICAL RESEARCH (SIP)--applications op
... Eligibility criteria are here: https://www2.training.nih.gov/apps/publicforms/sip/forms/sipapp.aspx . In short, I think your comment is correct. Also, note that this is not a "grant"; this is an internship that happens on one of the NIH intramural campuses (the largest is in Bethesda, MD, USA). ...
written 4 months ago by Sean Davis22k
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News: 2017 NIH SUMMER INTERNSHIP PROGRAM IN BIOMEDICAL RESEARCH (SIP)--applications open
... Applications are being accepted for the NIH Summer Internship Program: https://www.training.nih.gov/programs/sip Summer programs at the National Institutes of Health (NIH) provide an opportunity to spend a summer working at the NIH side-by-side with some of the leading scientists in the world, in ...
nih news training written 4 months ago by Sean Davis22k
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News: Upcoming workshop on the NCI Genomic Data Commons
... An upcoming workshop, run by the Genomic Data Commons User Services team, may be of interest to you. The workshop is intended for researchers with experience in genomics who want to learn more about how to use the GDC. Learn more about this event below: Date: Thursday, November 17th, 2016 Time: 12 ...
open data news data commons cancer written 4 months ago by Sean Davis22k
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Answer: A: gene name in vcf file
... I would suggest using a tool such as snpEff, annovar, Ensembl VEP, or the Bioconductor VariantAnnotation package for this task. ...
written 6 months ago by Sean Davis22k
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Comment: C: what are other possibilities apart from validation of retrieved data from GEO?
... What biological question are you trying to answer? Have you identified at least one dataset of interest? If so, what are you going to do to analyze that dataset? ...
written 6 months ago by Sean Davis22k
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Answer: A: fisher exact test
... I would suggest adopting a more standard approach such as edgeR, DESeq2, or limma voom. All of these are available from Bioconductor, are well-supported, have good documentation, and represent state-of-the-art approaches to testing for differential expression in RNA-seq. If you have something othe ...
written 6 months ago by Sean Davis22k
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Comment: C: How to annotate GEO microarray datasets with GEOquery?
... Unfortunately, this solution is not a general one due to the fact that not all GEO series have gene symbol or other annotation. What that means is that it is best to understand why the steps above work so that when you have another data set, you can follow the logic to come up with your own solution ...
written 6 months ago by Sean Davis22k
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Answer: A: How to annotate GEO microarray datasets with GEOquery?
... Take a look at this code: gse = gse[[1]] # get just the first element in the list head(fData(gse)) symbols = fData(gse)[,'Gene Symbol'] Now, you have the gene symbols. The gse object (after choosing the first element in the list using gse[[1]]) contains the information from the Series ...
written 6 months ago by Sean Davis22k

Latest awards to Sean Davis

Scholar 9 days ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Teacher 9 days ago, created an answer with at least 3 up-votes. For A: Separate Bam File
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: T-Test In R On Microarray Data
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Appreciated 3 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Perform Ge Analysis
Appreciated 3 months ago, created a post with more than 5 votes. For Bioconductor 2015 conference live tweeting and materials
Scholar 3 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
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Popular Question 3 months ago, created a question with more than 1,000 views. For Quick four-question survey on bioinformatics postdoc career path
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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
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Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Gene Lists Using Principal Component Analysis In Microarray Gene Expression
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: What Is Snp Calling?
Appreciated 5 months ago, created a post with more than 5 votes. For A: What Is Snp Calling?
Appreciated 5 months ago, created a post with more than 5 votes. For A: Going For The Right P-Value With Limma
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Scholar 6 months ago, created an answer that has been accepted. For A: How to get FASTQ files for diseased and receptive normal samples from TCGA datab
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Teacher 6 months ago, created an answer with at least 3 up-votes. For A: It Architecture For Large, Genomic Data-Backed Application

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