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Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis ♦ 26k
Reputation:
25,790
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, 2 weeks ago
Joined:
10 years, 9 months ago
Email:
s*******@gmail.com

Posts by Sean Davis

<prev • 2,015 results • page 1 of 202 • next >
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Job: Bioconductor and the Channing Division of Network Medicine at Harvard Medical School have created a new project management/software developer/manager position.
... 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, ...
bioinformatics bioconductor job written 3 months ago by Sean Davis ♦ 26k
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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 14 months ago by Sean Davis ♦ 26k
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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 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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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 17 months ago by Sean Davis ♦ 26k
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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 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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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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Answer: C: GEOquery getGEO() Error in open.connection(x, "rb") : HTTP error 403.
... It looks like the problem has been resolved. ...
written 21 months ago by Sean Davis ♦ 26k

Latest awards to Sean Davis

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Need Recommendations For Aligning Longer (2X250Bp) Reads
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Perform Ge Analysis
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: T-Test In R On Microarray Data
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Best Practices/Methods For Developing Bioinformatics Related Web Applications
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 14 months ago, created an answer that has been accepted. For A: Human 450K methylation data: Tumor vs Normal vs Control
Scholar 14 months ago, created an answer that has been accepted. For A: Genotyping by sequencing, Filtering Raw Sequence Data
Scholar 14 months ago, created an answer that has been accepted. For A: Question about gene fusion
Scholar 14 months ago, created an answer that has been accepted. For A: Unequal Sample Number
Scholar 14 months ago, created an answer that has been accepted. For A: Covariate Selection For Microarray Data
Scholar 14 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Scholar 14 months ago, created an answer that has been accepted. For A: Which Method Is The Best Dissimilarity Measurement For Hierarchical Clustering O
Popular Question 14 months ago, created a question with more than 1,000 views. For Availability of a robust, annotation-aware vcf-to-json converter
Popular Question 14 months ago, created a question with more than 1,000 views. For Bioinformatics Core Director, National Heart, Lung and Blood Institute, NIH
Popular Question 14 months ago, created a question with more than 1,000 views. For Quick four-question survey on bioinformatics postdoc career path
Popular Question 14 months ago, created a question with more than 1,000 views. For How can I serve a directory of BAM files via http most easily?
Popular Question 14 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Csv File Parsing With Perl
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: Why Do We Need Markduplicates For Variants Detection In Gatk Processing Pipeline
Appreciated 14 months ago, created a post with more than 5 votes. For A: Contribute To R Package Or Function In Cran
Appreciated 14 months ago, created a post with more than 5 votes. For A: False Positives In Disease Gene Hunting - Truseq Exome Enrichment Kit - A Call
Appreciated 14 months ago, created a post with more than 5 votes. For A: Assessing Whether Point Mutations Introduce Stop Codons Into Chromosomal Dna Usi
Appreciated 14 months ago, created a post with more than 5 votes. For A: Best Practices/Methods For Developing Bioinformatics Related Web Applications
Appreciated 14 months ago, created a post with more than 5 votes. For C: How To Be Helpful As A Biostar Moderator/Editor?
Scholar 14 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
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