Moderator: Sean Davis
Sean Davis ♦ 26k
- Reputation:
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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, 2 weeks ago
- Joined:
- 10 years, 9 months ago
- Email:
- s*******@gmail.com
Posts by Sean Davis
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... Bioconductor and the Channing Division of Network Medicine at Harvard Medical School have created a new project management/software developer/manager position. We are seeking candidates. Join an influential open source software project, interact with great scientists, and help manage a distributed, ...
written 3 months ago by
Sean Davis ♦ 26k
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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 14 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 15 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 17 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 17 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 17 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 17 months ago by
Sean Davis ♦ 26k
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651
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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 19 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 19 months ago by
Sean Davis ♦ 26k
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... It looks like the problem has been resolved. ...
written 21 months ago by
Sean Davis ♦ 26k
Latest awards to Sean Davis
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14 months ago,
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For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Teacher
14 months ago,
created an answer with at least 3 up-votes.
For A: T-Test In R On Microarray Data
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created an answer with at least 3 up-votes.
For A: Best Practices/Methods For Developing Bioinformatics Related Web Applications
Teacher
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For A: Varscan Snp Strand Information
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For A: Human 450K methylation data: Tumor vs Normal vs Control
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For A: Genotyping by sequencing, Filtering Raw Sequence Data
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For A: Covariate Selection For Microarray Data
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For A: Fasta File For Exomedepth And Cnv Calling
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For A: Which Method Is The Best Dissimilarity Measurement For Hierarchical Clustering O
Popular Question
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created a question with more than 1,000 views.
For Availability of a robust, annotation-aware vcf-to-json converter
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For Bioinformatics Core Director, National Heart, Lung and Blood Institute, NIH
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For Quick four-question survey on bioinformatics postdoc career path
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For A: Csv File Parsing With Perl
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