User: gabt

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gabt100
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Posts by gabt

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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... can I ask if you have some references regarding the topic? ...
written 13 days ago by gabt100
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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... ok, that is clear, stick to GO and verify similarity between genes. Also, thanks for the link! ...
written 13 days ago by gabt100
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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... So basically they just did a symbol transoformation from one organism to another without considering homology/orthology but just assuming that it is ok to do so, right? Is this meaningful? I suppose it can be since mouse is used as animal model but eventually things that work out for mice do not alw ...
written 14 days ago by gabt100
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Comment: C: is it meaningful to enrich an organism using ontology from a different organism?
... Ok, so basically whenever I need to perform an enrichment I should verify if there is a specific amount of similarity between the genes in the different organism. If this similarity is not significant enough I must assume that the enrichment will not provide meaningful results. Is that correct? ...
written 14 days ago by gabt100
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is it meaningful to enrich an organism using ontology from a different organism?
... Suppose I have a list of genes obtained from an experiment using mice. Now I have to perform an enrichment and I can choose to perform it using mouse GO terms, human GO terms, etc... Is it ok to use human GO terms over mice genes? If yes, then why bother creating specific mouse GO terms? I underst ...
enrichment geneontology written 15 days ago by gabt100 • updated 15 days ago by Papyrus550
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Answer: A: how can i convert factor to numeric in shiny
... see this [link][1]. It may help you understanding how factors work in R. Also, it would be nice to have a small example of what you tried to do, so that people can help you improving your code. [1]: https://stackoverflow.com/questions/3418128/how-to-convert-a-factor-to-integer-numeric-without-lo ...
written 8 months ago by gabt100
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Answer: A: Tripartite Network Construction
... according to your last comment, you just need a visual representation of the network. There are many ways to achieve this goal but Cytoscape can be the easiest way to go. First problem: which format is your network? Do you have a file with two columns, where each row represent an interaction? We ne ...
written 8 months ago by gabt100
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Comment: C: How to plot GSEA result?
... which plot of the many listed in the tutorial are you referring to? ...
written 12 months ago by gabt100
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Answer: A: How to plot GSEA result?
... I have been working on GSEA too and I found two very interesting resources but I am not that proficient with this kind of analysis so I am still not able to interpret the plots. However, here you can find a [very nice tutorial for R][1] that gives you some plotting. Also there is a [question][2] an ...
written 12 months ago by gabt100
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Answer: A: Software to reconstruct a proteomics-based metabolic pathway
... I am a great fan of R and there are plenty of libraries to actually do bioinformatics. In this specific case I would recommend using the **pathview** library (see [this link][1] or [this other link][2] for some examples and help) just to give you some working code that you may test, if you are fami ...
written 12 months ago by gabt100

Latest awards to gabt

Scholar 12 months ago, created an answer that has been accepted. For A: Concatenation of sequences (fasta) with different headers based on reference lis
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: How to plot GSEA result?
Scholar 12 months ago, created an answer that has been accepted. For A: Concatenation of sequences (fasta) with different headers based on reference lis
Scholar 12 months ago, created an answer that has been accepted. For A: Concatenation of sequences (fasta) with different headers based on reference lis

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