Moderator: Sean Davis
Sean Davis ♦ 24k
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- http://watson.nci.nih....
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Posts by Sean Davis
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... 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 4 weeks ago by
Sean Davis ♦ 24k
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... 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 ...
written 7 weeks ago by
Sean Davis ♦ 24k
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... 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 7 weeks ago by
Sean Davis ♦ 24k
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144
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... What data are you trying to get? Gene expression, clinical? ...
written 7 weeks ago by
Sean Davis ♦ 24k
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124
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... GSE18 has nine different platforms (microarray types). The GDS records each represent one of those microarray types. ...
written 7 weeks ago by
Sean Davis ♦ 24k
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1
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124
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... 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 7 weeks ago by
Sean Davis ♦ 24k
1
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3
answers
768
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3
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... [netsig](https://www.nature.com/articles/nmeth.4514) is a new one. ...
written 7 weeks ago by
Sean Davis ♦ 24k
1
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0
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252
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... 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 7 weeks ago by
Sean Davis ♦ 24k
1
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0
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143
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0
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... Why not just remove NA values? ...
written 7 weeks ago by
Sean Davis ♦ 24k
0
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1
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176
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... Feel free to "accept" the answer so that others know that the question is answered. : ) ...
written 7 weeks ago by
Sean Davis ♦ 24k
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For Clients to access TCGA data from R and Python
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For National Institutes of Health tenure-track recruitment
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For Clients to access TCGA data from R and Python
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For Clients to access TCGA data from R and Python
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created a question with more than 1,000 views.
For Clients to access TCGA data from R and Python
Popular Question
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For Clients to access TCGA data from R and Python
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