Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis25k
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Location:
National Institutes of Health, Bethesda, MD
Website:
http://watson.nci.nih....
Twitter:
seandavis12
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Google Scholar Page
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1 month ago
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9 years, 2 months ago
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Posts by Sean Davis

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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 Davis25k
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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 Davis25k
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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 Davis25k
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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 Davis25k
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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 Davis25k
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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 Davis25k
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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 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 9 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 11 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 15 months ago by Sean Davis25k

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Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
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