User: restonpiston

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restonpiston30
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Posts by restonpiston

<prev • 11 results • page 1 of 2 • next >
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KGML to SVG
... Hello everyone! I was trying to improve my pipeline and I was wondering if there is any tool convert KGML tools into SVG files or similar format in an automated way (i.e from terminal). ...
pathway automation kegg svg written 9 months ago by restonpiston30
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Answer: A: Suggestions for avoiding False Positives while identifying differentially expres
... First of all, it is not advisable to check for DEG between the replicates themselves, unless you have a very good reason for it (you know one of them were treated differently, etc.). I would also advice that you limit your efforts to comparisons between the categories, as they will provide more mean ...
written 11 months ago by restonpiston30
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Comment: C: GO enrichment tools
... Hello restonpiston! We believe that this post does not fit the main topic of this site. Found a tool that suited my needs For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in ...
written 11 months ago by restonpiston30
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Comment: C: GO enrichment tools
... I checked it out, very nice tool, what I needed to be honest! The only disadvantage is that I had to unravel the obo file to annotate the genes also to the ancestors, but after doing so I could test enrichment and gene set quite easily. ...
written 11 months ago by restonpiston30
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Comment: C: GO enrichment tools
... I have updated my answer, I was not very specific, you are right ...
written 11 months ago by restonpiston30
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(Closed) GO enrichment tools
... Hello everyone! I have recently started to analyze RNA-seq data and I would like to know which tools are current now for the purpose of GO enrichment. I have checked out topGO, BiNGO, and building my own hypergeometric test, but none really satisfied me. I am looking for suggestions of tools that ...
R rna-seq go written 11 months ago by restonpiston30 • updated 11 months ago by EagleEye6.6k
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Answer: A: GeneId to GO terms
... First you have to download the GAF file corresponding to your species from [here][1] Then you can run this small script to get the GO terms you are looking for. data<-read.delim(file="input/sgd.gaf",sep = "\t", as.is=TRUE, header=FALSE, comment.char="!") data<-data[,c("V5","V9","V11" ...
written 11 months ago by restonpiston30
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Answer: A: Interpreting GSEA enrichment plots/results
... I was in your position a few weeks ago, and I found [this link][1] from GSEA in the generated report. The peak point of the green plot is your ES (enrichment score), which tells you how over or under expressed is your gene respect to the ranked list. The second part of the graph (middle with red ...
written 11 months ago by restonpiston30
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Comment: C: GSEA Tool to use with RNA-seq data
... Thanks for the answer! I have managed to use it and it works pretty well, even tho I had to modify my data a bit, as I am using custom pathway annotations. ...
written 11 months ago by restonpiston30
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Comment: C: GSEA Tool to use with RNA-seq data
... Thanks for the answer! Unfortunately, I do not seem to be able to have it working. I have input the data like this: ![WebGestalt Saccharomyces][1] Maybe you could tell me what I am doing wrong? I am receiving "R error (1565083554)". [1]: https://i.imgur.com/wBYMnQA.png ...
written 11 months ago by restonpiston30

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