Moderator: Sean Davis
Sean Davis ♦ 26k
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- Location:
- National Institutes of Health, Bethesda, MD
- Website:
- http://watson.nci.nih....
- Twitter:
- seandavis12
- Scholar ID:
- Google Scholar Page
- Last seen:
- 3 months ago
- Joined:
- 9 years, 10 months ago
- Email:
- s*******@gmail.com
Posts by Sean Davis
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... If you are using R, you could consider looking at the GenomicDataCommons package to help facilitate finding and downloading datasets of interest. However, Kevin is correct that the MAFs are probably what you want. Note the the MAFs are filtered from the original variant files which are available onl ...
written 3 months ago by
Sean Davis ♦ 26k
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... Downloading the supplemental files from the GEO website (or using GEOquery) will get you the files. From there, you'll have to determine the best way to parse them. ...
written 4 months ago by
Sean Davis ♦ 26k
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Comment:
C: NCBI SRA AWS AMI
... I believe that SRA toolkit will remain as an option, at least for the foreseeable future. I know of *no* SRA datasets that are available in the cloud *only* as of now. ...
written 6 months ago by
Sean Davis ♦ 26k
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... Your code looks OK. What are the dimensions of `my_eset_norm_just_miRNA`? ...
written 6 months ago by
Sean Davis ♦ 26k
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... If there are three files, they are paired. The metadata from SRA is not uncommonly incorrect. ...
written 6 months ago by
Sean Davis ♦ 26k
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Answer:
A: NCBI SRA AWS AMI
... Here is what I got from SRA about a week ago. In short, you'll likely need an AWS or GCP account and you may need to pay download costs unless you are using the data in the cloud. Full documentation is apparently being prepared.
> The SRA Toolkit is needed for ETL data and the default toolkit co ...
written 6 months ago by
Sean Davis ♦ 26k
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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 8 months ago by
Sean Davis ♦ 26k
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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 8 months ago by
Sean Davis ♦ 26k
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... It looks like the problem has been resolved. ...
written 10 months ago by
Sean Davis ♦ 26k
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... 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 10 months ago by
Sean Davis ♦ 26k
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