User: predeus

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predeus0
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Posts by predeus

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Comment: C: topGO - treating up- and down-regulated genes separately
... yeah, it's pretty clear how it works for Fisher's statistics and the like - you just select the genes you consider significant and calculate the p-value for 2x2 table it's much more tricky for KS (or KS-like, as in GSEA) - statistic should add up some statistic (in some power) to the running sum, r ...
written 2.5 years ago by predeus0
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Answer: A: pre-ranked GSEA within R: options?
... use fgsea package on Bioconductor ...
written 2.5 years ago by predeus0
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topGO - treating up- and down-regulated genes separately
... I've recently started using topGO in my expression analysis and like it a lot. The "elimination" paradigm is a very useful one when doing pathway analysis, since many different pathways do in fact overlap in the genes they contain.  In the manual, all the examples are using p-values as a statistic, ...
topgo pathway analysis gsea written 2.5 years ago by predeus0 • updated 2.5 years ago by Lluís Revilla Sancho500
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Answer: A: how to perform pre ranked GSEA in R?
... use fgsea bioconductor package. ...
written 2.5 years ago by predeus0
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GO.db installation error
... Hello all, I've been trying to install WGCNA on our cluster. It has module system, so I've chosen R-3.1.2 and installed bunch of libs locally (which all worked OK). Now, GO.db was the only one that failed to install. When I typed source("https://bioconductor.org/biocLite.R") biocLite("GO.db") ...
go sqlite written 3.8 years ago by predeus0 • updated 3.8 years ago by Daniel Lai0

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Popular Question 2.5 years ago, created a question with more than 1,000 views. For GO.db installation error

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