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Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis ♦ 25k
Reputation:
25,130
Status:
Trusted
Location:
National Institutes of Health, Bethesda, MD
Website:
http://watson.nci.nih....
Twitter:
seandavis12
Scholar ID:
Google Scholar Page
Last seen:
1 month ago
Joined:
9 years, 2 months ago
Email:
s*******@gmail.com

Posts by Sean Davis

<prev • 2,008 results • page 1 of 201 • next >
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Comment: C: How to create own SRAdb
... Unfortunately, I do not have direct access to SRA. I mine the data from multiple publicly available locations at NCBI in what is a non-trivial exercise. ...
written 4 weeks ago by Sean Davis ♦ 25k
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Answer: A: How to create own SRAdb
... Due to growing size of SRA metadata, we have been transitioning to a new approach for building, updating, and distributing the SRA metadata. As a first step, the data are available as public resource on Google BigQuery. https://seandavi.github.io/2019/06/omicidx-on-bigquery/ Access BigQuery via an ...
written 4 weeks ago by Sean Davis ♦ 25k
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Answer: C: GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.
... It looks like the problem has been resolved. ...
written 11 weeks ago by Sean Davis ♦ 25k
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Comment: C: GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.
... Just to be clear, the reported problem here is due to a problem at NCBI, not with GEOquery. Until NCBI resolves its network/hosting issues, access via GEOquery will not work. ...
written 11 weeks ago by Sean Davis ♦ 25k
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Comment: C: GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.
... I would suggest reporting issues to NCBI GEO staff (geo@ncbi.nlm.nih.gov). I agree that recent behavior of GEO has been more spotty than previous. ...
written 11 weeks ago by Sean Davis ♦ 25k
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Answer: A: Where Can I Find Mutation Databases Specialized In Cancer?
... Perhaps not a direct answer, but take a look at: https://github.com/seandavi/awesome-cancer-variant-databases ...
written 3 months ago by Sean Davis ♦ 25k
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Answer: A: GenomicDataCommons request timeouts cases() %>% ... %>% results_all()
... I should clean up the documentation, but `results_all()` is a convenience wrapper that is not too smart in that it simply tries to return all results in one trip to the server. This can fail for multiple reasons related to the size of result sets. The better approach (and the only one in the case of ...
written 6 months ago by Sean Davis ♦ 25k
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Answer: C: Using GenomicDataCommons R package to identify cases with both DNA methylation a
... See: https://support.bioconductor.org/p/114340/#114357 for the answer. ...
written 9 months ago by Sean Davis ♦ 25k
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Answer: A: count tables from RNA-seq data on GEOmetadb
... GEOmetadb contains only the "metadata", not the actual RNA-seq counts. You can use GEOquery to access the actual data, if they have been submitted, or you can download fastq from SRA if you have access to the studies (since it appears you are working in human, these files will be protected). ...
written 11 months ago by Sean Davis ♦ 25k
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Comment: C: Protocol To Downlad TCGA Data From GDC
... The ICGC is not the right place to get access to TCGA controlled-access data, as you point out. To gain access to controlled-access TCGA data, one needs to apply through dbGaP. The process is documented here: https://gdc.cancer.gov/access-data/obtaining-access-controlled-data After approval for co ...
written 15 months ago by Sean Davis ♦ 25k

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Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 11 weeks ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Good Answer 11 weeks ago, created an answer that was upvoted at least 5 times. For A: Where Should I Start From ?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 3 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Appreciated 3 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Where Can I Find Mutation Databases Specialized In Cancer?
Great Question 5 months ago, created a question with more than 5,000 views. For Snakemake--Python-Based Workflow Management
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 8 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Appreciated 8 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Scholar 11 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Popular Question 11 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH
Popular Question 11 months ago, created a question with more than 1,000 views. For Brief Getting Started with Broad Firecloud tutorial posted
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: What Coverage Is Required For Chip-Seq Experiments?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: How To Download All Sra Samples At Once ?
Good Question 11 months ago, asked a question that was upvoted at least 5 times. For What Are The Big Questions That Bioinformatics And Computational Biology Will Be Answering In The Next Few Years?
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Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 14 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
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