Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis26k
Reputation:
25,500
Status:
Trusted
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

<prev • 2,014 results • page 1 of 202 • next >
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Comment: C: Extracting VCF of all variants in TCGA exomes from all cancer types
... 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 Davis26k
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Comment: C: Cannot read Illumina data (.bgx and .txt format) in R for microanalysis
... 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 Davis26k
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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 Davis26k
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Comment: C: extracting a subset of probes from an expression object
... Your code looks OK. What are the dimensions of `my_eset_norm_just_miRNA`? ...
written 6 months ago by Sean Davis26k
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Answer: A: ENA fastq file shown as single-end but has 3 fastq files: X.fastq.gz X_1.fastq.g
... If there are three files, they are paired. The metadata from SRA is not uncommonly incorrect. ...
written 6 months ago by Sean Davis26k
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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 Davis26k
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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 Davis26k
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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 Davis26k
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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 10 months ago by Sean Davis26k
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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 10 months ago by Sean Davis26k

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