Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis25k
Reputation:
25,340
Status:
Trusted
Location:
National Institutes of Health, Bethesda, MD
Website:
http://watson.nci.nih....
Twitter:
seandavis12
Scholar ID:
Google Scholar Page
Last seen:
3 weeks ago
Joined:
9 years, 6 months ago
Email:
s*******@gmail.com

Posts by Sean Davis

<prev • 2,013 results • page 1 of 202 • next >
0
votes
1
answer
4.7k
views
1
answers
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 26 days ago by Sean Davis25k
0
votes
1
answer
481
views
1
answers
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 3 months ago by Sean Davis25k
0
votes
0
answers
214
views
0
answers
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 3 months ago by Sean Davis25k
2
votes
1
answer
196
views
1
answers
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 3 months ago by Sean Davis25k
3
votes
1
answer
481
views
1
answers
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 3 months ago by Sean Davis25k
0
votes
1
answer
321
views
1
answers
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 months ago by Sean Davis25k
2
votes
1
answer
321
views
1
answers
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 months ago by Sean Davis25k
1
vote
1
answer
838
views
1
answers
Answer: C: GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.
... It looks like the problem has been resolved. ...
written 6 months ago by Sean Davis25k
1
vote
1
answer
838
views
1
answers
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 6 months ago by Sean Davis25k
1
vote
1
answer
838
views
1
answers
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 6 months ago by Sean Davis25k

Latest awards to Sean Davis

Scholar 26 days ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Scholar 3 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Popular Question 3 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH
Appreciated 3 months ago, created a post with more than 5 votes. For C: How To Be Helpful As A Biostar Moderator/Editor?
Scholar 4 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Librarian 4 months ago, created a post with more than 10 bookmarks. For Introduction To R Course Materials Available
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 6 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Where Should I Start From ?
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 7 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Appreciated 7 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Where Can I Find Mutation Databases Specialized In Cancer?
Great Question 8 months ago, created a question with more than 5,000 views. For Snakemake--Python-Based Workflow Management
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Commentator 9 months ago, created a comment with at least 3 up-votes. For C: How To Be Helpful As A Biostar Moderator/Editor?
Scholar 9 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
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
Appreciated 12 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Scholar 15 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Popular Question 15 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2132 users visited in the last hour