Moderator: Sean Davis

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Sean Davis25k
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National Institutes of Health, Bethesda, MD
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http://watson.nci.nih....
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Posts by Sean Davis

<prev • 2,002 results • page 1 of 201 • next >
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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 8 weeks ago by Sean Davis25k
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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 4 months ago by Sean Davis25k
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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 7 months ago by Sean Davis25k
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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 11 months ago by Sean Davis25k
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News: Invitation to submit articles to the Bioconductor Gateway on F1000Research
... We invite you to contribute to a series of articles that will accompany the BioC 2018 conference in the [Bioconductor gateway on F1000Research][1]. We are specifically looking for: - Cross-package workflows - Package-based vignettes that show how to solve a scientific problem end-to-end - Teaching ...
bioconductor news written 11 months ago by Sean Davis25k
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Answer: A: Comparing two RNA-seq datasets of same species and treatments
... Using a GSEA approach where one study's DEG list is the "gene set" which you can test for enrichment in the other will give you a statistical result. I think this is one answer for both of your questions. There are other ways to look at individual gene-level results, including meta-analysis. ...
written 11 months ago by Sean Davis25k
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Comment: C: Data Discrepency from TCGA-GDC portal and GDC firehose
... What data are you trying to get? Gene expression, clinical? ...
written 11 months ago by Sean Davis25k
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Comment: C: Differentiation in GSE and GDS idS
... GSE18 has nine different platforms (microarray types). The GDS records each represent one of those microarray types. ...
written 11 months ago by Sean Davis25k
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Answer: A: Differentiation in GSE and GDS idS
... Some submissions have undergone a curation process at GEO, giving them a GDS accession. NCBI has not been curating data for several years, so the GDS accessions are historical and now represent a pretty small proportion of the GEO information. A GDS and GSE represent pretty much the same type of dat ...
written 11 months ago by Sean Davis25k
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Answer: A: Tool/algorithm to assess the effect of several mutations
... [netsig](https://www.nature.com/articles/nmeth.4514) is a new one. ...
written 11 months ago by Sean Davis25k

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Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
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Scholar 7 weeks ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
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Scholar 7 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Popular Question 7 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH
Popular Question 7 months ago, created a question with more than 1,000 views. For Brief Getting Started with Broad Firecloud tutorial posted
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Popular Question 10 months ago, created a question with more than 1,000 views. For Brief Getting Started with Broad Firecloud tutorial posted
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: What Is Snp Calling?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Appreciated 11 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
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 Clients to access TCGA data from R and Python
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 12 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling

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