Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis25k
Reputation:
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Location:
National Institutes of Health, Bethesda, MD
Website:
http://watson.nci.nih....
Twitter:
seandavis12
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Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
8 years, 4 months ago
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Posts by Sean Davis

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Answer: A: count tables from RNA-seq data on GEOmetadb
... GEOmetadb contains only the "metadata", not the actual RNA-seq counts. You can use GEOquery to access the actual data, if they have been submitted, or you can download fastq from SRA if you have access to the studies (since it appears you are working in human, these files will be protected). ...
written 7 weeks ago by Sean Davis25k
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Comment: C: Protocol To Downlad TCGA Data From GDC
... The ICGC is not the right place to get access to TCGA controlled-access data, as you point out. To gain access to controlled-access TCGA data, one needs to apply through dbGaP. The process is documented here: https://gdc.cancer.gov/access-data/obtaining-access-controlled-data After approval for co ...
written 5 months ago by Sean Davis25k
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News: Invitation to submit articles to the Bioconductor Gateway on F1000Research
... We invite you to contribute to a series of articles that will accompany the BioC 2018 conference in the [Bioconductor gateway on F1000Research][1]. We are specifically looking for: - Cross-package workflows - Package-based vignettes that show how to solve a scientific problem end-to-end - Teaching ...
bioconductor news written 5 months ago by Sean Davis25k
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Answer: A: Comparing two RNA-seq datasets of same species and treatments
... Using a GSEA approach where one study's DEG list is the "gene set" which you can test for enrichment in the other will give you a statistical result. I think this is one answer for both of your questions. There are other ways to look at individual gene-level results, including meta-analysis. ...
written 5 months ago by Sean Davis25k
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Comment: C: Data Discrepency from TCGA-GDC portal and GDC firehose
... What data are you trying to get? Gene expression, clinical? ...
written 5 months ago by Sean Davis25k
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Comment: C: Differentiation in GSE and GDS idS
... GSE18 has nine different platforms (microarray types). The GDS records each represent one of those microarray types. ...
written 6 months ago by Sean Davis25k
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Answer: A: Differentiation in GSE and GDS idS
... Some submissions have undergone a curation process at GEO, giving them a GDS accession. NCBI has not been curating data for several years, so the GDS accessions are historical and now represent a pretty small proportion of the GEO information. A GDS and GSE represent pretty much the same type of dat ...
written 6 months ago by Sean Davis25k
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Answer: A: Tool/algorithm to assess the effect of several mutations
... [netsig](https://www.nature.com/articles/nmeth.4514) is a new one. ...
written 6 months ago by Sean Davis25k
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Comment: C: Differential expression gene analysis
... What is the classifier you want to build? And what samples will you be classifying, relative to the DESeq2 analysis--different samples or the same samples? ...
written 6 months ago by Sean Davis25k
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Comment: C: Hierarchical Clustering of copy number variations
... Why not just remove NA values? ...
written 6 months ago by Sean Davis25k

Latest awards to Sean Davis

Teacher 4 months ago, created an answer with at least 3 up-votes. For A: T-Test In R On Microarray Data
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Best Practices/Methods For Developing Bioinformatics Related Web Applications
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 4 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Popular Question 4 months ago, created a question with more than 1,000 views. For Brief Getting Started with Broad Firecloud tutorial posted
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: What Is Snp Calling?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Appreciated 5 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Popular Question 5 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH
Popular Question 6 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
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
Appreciated 6 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Scholar 6 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Popular Question 6 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Scholar 6 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Scholar 6 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Popular Question 6 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Popular Question 6 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Popular Question 6 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Best Practices/Methods For Developing Bioinformatics Related Web Applications
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
Scholar 7 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling

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