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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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 3 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 3 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 3 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 5 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 5 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 5 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 5 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 5 months ago by Sean Davis22k
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Answer: C: Extracting SNPs that differ in genotype between two individuals.
... Yes, but you will probably need to do that using R, python, or some other language. It could be done in Excel, I suspect, but I wouldn't recommend that approach. ...
written 6 months ago by Sean Davis22k
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Answer: A: TCGA data set with both expression (rna seq/ microarray) and exome seq of same
... TCGA has both gene expression and exome/genome sequence data for nearly all samples. To get access to the actual sequencing data, you will need to apply for access, as sequencing data for human subjects is almost always controlled access. See here for instructions: https://wiki.nci.nih.gov/displa ...
written 6 months ago by Sean Davis22k

Latest awards to Sean Davis

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Gene Lists Using Principal Component Analysis In Microarray Gene Expression
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Is Snp Calling?
Appreciated 4 months ago, created a post with more than 5 votes. For A: What Is Snp Calling?
Popular Question 4 months ago, created a question with more than 1,000 views. For Cross-Posting To Here And Email Lists
Appreciated 4 months ago, created a post with more than 5 votes. For A: Going For The Right P-Value With Limma
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Going For The Right P-Value With Limma
Scholar 5 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
Teacher 5 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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Scholar 5 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
Scholar 5 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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Popular Question 6 months ago, created a question with more than 1,000 views. For Predict Oncogenic Potential Of Snv
Popular Question 6 months ago, created a question with more than 1,000 views. For Snakemake--Python-Based Workflow Management
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Popular Question 7 months ago, created a question with more than 1,000 views. For Cnv Annotation Tools
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Is There Any R Or R / Bioconductor Package That Can Make Circular Plots Like Per
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How To Download All Sra Samples At Once ?
Appreciated 9 months ago, created a post with more than 5 votes. For The NIH Software Discovery Index | We invite your comments
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