User: assaron

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assaron110
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assaron
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Posts by assaron

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Cut-off for genesets in GSEA
... Cut-offs are more of performance parameters. Limiting min and max set sizes you limit the time required for the analysis. For large gene sets estimation of is computationally harder compared to smaller gene sets. ...
written 8 weeks ago by assaron110
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Answer: A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler
... I'd recommend changing infinities to the corresponding maximum positive and negative finite values, may be multiplied by a constant > 1. GSEA here is about weighted ranking: you can assign it whatever you like and it would be fine from the method's standpoint. However, when you remove some genes ...
written 3 months ago by assaron110
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Comment: C: GSEA following DESeq2
... As you use R pipeline, I recommend to use R implementation of pre-ranked GSEA: either through fgsea package or clusterprofiler/DOSE interface. It's the same method but much faster. Answering your question, I normally use stat column of DESeq2 results, but your metric should also work fine. ...
written 5 months ago by assaron110
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Comment: C: How do I obtain germline mutation for TCGA samples?
... Yes. You still need a key for the protected data. ...
written 5 months ago by assaron110
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Answer: A: Input all the ranked genes into pre-ranked GSEA?
... While you indeed can input all your genes into GSEA, personally usually select top 12000 expressed genes. This allows to reduce noise from lowly-expressed and non-expressed genes. ...
written 6 months ago by assaron110
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Answer: A: How do I obtain germline mutation for TCGA samples?
... The only way that worked for me was to go to GDC Legacy Archive and download protected vcfs from there. In the new version I couldn't find germline mutation calls anywhere, even in protected MAFs and VCFs. ...
written 7 months ago by assaron110
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Answer: A: How to view all KEGG reactions?
... You can get up-to-date links between kegg reaction IDs and genes using KEGG REST API. You can first find mapping from reactions to enzymes and then from enzymes to human genes: library(KEGGREST) rxn2enz <- keggLink("enzyme", "reaction") enz2hsa <- keggLink("hsa", "enzyme") Replac ...
written 10 months ago by assaron110
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Answer: A: GSEA genesets postiively enriched in positive phenotype are necessarily negative
... AFAIK, there is no positive enrichement in positive phenotype: it's either positive enrichment, or enrichment in positive phenotype. Each pathway can be either positevely enriched (with positive ES score) or negatively enriched. ...
written 14 months ago by assaron110
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Answer: A: Trimming redundant gene sets after gsea analysis
... One of the things I was playing with to reduce redundant gene sets was bayesian-network-like filtering. There is example of it here: https://gist.github.com/assaron/6d2beb89ed2a89723c5796be87a0e2e5 The idea is the following. Let's consider two enriched overlapping pathways p1 and p2. First, let's m ...
written 15 months ago by assaron110
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Comment: C: Simplest way to perform GSEA from a weighted list of entrez gene ids
... Assuming you have downloaded files https://raw.githubusercontent.com/ctlab/fgsea/master/inst/extdata/naive.vs.th1.rnk and https://raw.githubusercontent.com/ctlab/fgsea/master/inst/extdata/mouse.reactome.gmt into your working directory, this should work rnk.file <- "naive.vs.th1.rnk" gmt ...
written 18 months ago by assaron110

Latest awards to assaron

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: How to handle the 'Inf' and '-Inf' in cufflinks output when use clusterprofiler

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