Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis24k
Reputation:
24,420
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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:
2 months ago
Joined:
8 years, 2 months ago
Email:
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Posts by Sean Davis

<prev • 1,999 results • page 1 of 200 • next >
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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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 3 months ago by Sean Davis24k
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Comment: C: Hierarchical Clustering of copy number variations
... Why not just remove NA values? ...
written 3 months ago by Sean Davis24k
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Comment: C: Finding and plotting gaps in denovo assembly in R
... Feel free to "accept" the answer so that others know that the question is answered. : ) ...
written 3 months ago by Sean Davis24k

Latest awards to Sean Davis

Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Appreciated 3 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
Popular Question 3 months ago, created a question with more than 1,000 views. For Staff Scientist, Laboratory of Genome Integrity, NCI, NIH
Popular Question 3 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 3 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Appreciated 3 months ago, created a post with more than 5 votes. For National Institutes of Health tenure-track recruitment
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 Clients to access TCGA data from R and Python
Scholar 4 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Scholar 4 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Popular Question 4 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Popular Question 4 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Popular Question 4 months ago, created a question with more than 1,000 views. For Clients to access TCGA data from R and Python
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Best Practices/Methods For Developing Bioinformatics Related Web Applications
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Scholar 5 months ago, created an answer that has been accepted. For A: Fasta File For Exomedepth And Cnv Calling
Scholar 5 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: in R, how to get the gene symbols of GPL
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Varscan Snp Strand Information
Popular Question 7 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: What Figure You Make For Qc Of Whole Exome Sequencing Data
Scholar 7 months ago, created an answer that has been accepted. For C: how to cluster genes in heatmap
Scholar 7 months ago, created an answer that has been accepted. For C: how to cluster genes in heatmap

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