User: kelen

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kelen160
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Posts by kelen

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Comment: C: Duplicated genes in overrepresentation analysis (ORA)
... This is just coming from what I know about ORA as I thought this is what you were asking, if you are instead looking for something WES and mutation specific then there might be other approaches. For best practices in checking for enrichment through ORA in a simple gene list would require using uniq ...
written 5 weeks ago by kelen160
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Answer: A: Duplicated genes in overrepresentation analysis (ORA)
... If I understand you correctly you want an ORA tool that would accept a list of genes that has duplicated genes? In that case it might be easier to just input a gene list that only has unique values and not guess if the tool does any filtering. You can filter your gene list to only report back unique ...
written 5 weeks ago by kelen160
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Comment: C: fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
... Thank you so much! This is perfect, really helpful. A good take home message for myself is then to not play around with every parameter. But in case I want to do so, now I know what effect this has. ...
written 9 weeks ago by kelen160
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Answer: A: GSEA Pre-ranked for an Overlapped Gene Set
... I haven't come across (yet) anyone doing GSEA on overlaps exactly for the reason you mention, that they need to be ranked somehow. This kind of leaves you with over representation analysis (ORA). I would suggest checking what happens when you do ORA on these gene lists. I quite like gprofiler for t ...
written 10 weeks ago by kelen160
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fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
... Hi! Fgsea has recently moved to using fgseaMultilevel by default and from what I understand does not use sampling for p-value calculations, but instead an "adaptive multilevel splitting Monte Carlo approach. " (from the documentation). I have been trying to understand some of the new arguments incl ...
fgsea gsea rna-seq functional enrichment analysis written 10 weeks ago by kelen160
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Comment: C: impulseDE2 result table
... For Q1. If it helps, he has addressed the same question on Github - https://github.com/YosefLab/ImpulseDE2/issues/5 Q2. If I remember correctly I never figured out an easy way to do this, but if you check the source code for the heatmap (https://github.com/YosefLab/ImpulseDE2/blob/master/R/srcImpul ...
written 10 weeks ago by kelen160
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Answer: A: Is there a way to visualize log fold changes for Reactome pathways in R?
... One potential way I found for doing this is through using the Wikipathways .gpml version of Reactome pathways and Pathvisio. It won't preserve the exact coloring scheme, but that might be manually possible in Pathvisio. For a quick test-run I just downloaded a pathway from here (https://www.wikipath ...
written 11 weeks ago by kelen160
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Comment: C: Is there a way to visualize log fold changes for Reactome pathways in R?
... Thanks for the clarification and the additional tips, Jared! ...
written 3 months ago by kelen160
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Comment: C: Is there a way to visualize log fold changes for Reactome pathways in R?
... Sorry, that was unintentional, but completely my bad! Thanks for fixing it. Since there were no solutions to this here, I was not sure how else to contact Gabriel to ask if maybe they had figured this out. Is commenting on an un-answered thread to get it back on the 'latest' queue and potentially ...
written 3 months ago by kelen160
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Comment: A: Is there a way to visualize log fold changes for Reactome pathways in R?
... Hi, Gabriel! Any chance you found out how to do this? ...
written 3 months ago by kelen160

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