User: Ricardo Silva

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Ricardo Silva110
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Posts by Ricardo Silva

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Retrieve GO terms for organism without complete genomes and do enrichment by myself
... Hi, I'm working with a fungus that don't have its genome sequenced. I have a list of accession numbers from a blast of peptides obtained from a proteomics experiment, and each number come from a different organism. For what I read until now, I found how to recover GO terms for organism specific da ...
go organism written 5.8 years ago by Ricardo Silva110 • updated 5.8 years ago by Marc Carlson7.2k
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Retrieve GO terms for unanontaded organism and do enrichment by myself
... Hi, I'm working with a fungus that don't have its genome sequenced. I have a list of accession numbers from a proteomics experiment, and each number come from a different organism. For what I read until now, I found how to recover GO terms for organism specific databases as in: org.Mm.egGO[mapped ...
proteomics go organism written 5.8 years ago by Ricardo Silva110
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Doubt RCytoscape
... I'm exporting graph from R to cytoscape, and then importing attribute tables. In my problem each node has a set of attributes, but this attributes will be ideally displayed as in http://labpib.fmrp.usp.br/~rsilva/fabien/rattus.html 304.239771238418 w hydroxy testosterone ...
graph written 6.3 years ago by Ricardo Silva110 • updated 6.3 years ago by Paul Shannon750
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Comment: C: Quick questions about RCytoscape
... Hi Paul, thank you, sorry for the unfocused question again. I was thinking in export graphs in .sif from R, like this one http://metexplore.toulouse.inra.fr/metexploreJoomla/metexplore/tmp/gra ph_1584167971.sif maybe some one already did that. So exporting a file like this I could send to a coll ...
written 6.4 years ago by Ricardo Silva110
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Answer: A: KEGGgraph
... Hi Paul, thank you very much for spending your time to help me. Bellow I will try to follow your ideas On Tue, Oct 30, 2012 at 5:25 PM, Paul Shannon wrote: > Hi Ricardo, > > We might not be able to give you just what you need right away, but your > questions are very useful, helping ...
written 6.8 years ago by Ricardo Silva110
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Answer: A: KEGGgraph
... Hi Paul, thanks for answering. I'm already a RCytoscape user, it's very great, but I still have to spend some time customizing the graphs. I agree with your point about kegg, but is still the most comprehensive (reactome: http://www.reactome.org/stats.html and kegg: http://www.kegg.jp/kegg/docs/s ...
written 6.8 years ago by Ricardo Silva110
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KEGGgraph
... Hello all, I've been trying to create the most complete possible compound map for an organism, and KEGGgraph was the best approach until now. Someone already worked with graphs metabolites in R? I have a doubt if the KEGGgraph merging process can miss nodes, that's because, looking at the compoun ...
pathways organism graph process kegggraph written 6.8 years ago by Ricardo Silva110
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Answer: A: KEGGSOAP
... Hi everyone, I've added a function that I need to the KEGGSOAP package (in bold), as a copy of an existing function, bellow, in the KEGGSOAP.R, and then installed the function successfully, but I got this error message when I am installing or loading the package Note: Method with signature "Primit ...
written 7.5 years ago by Ricardo Silva110
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Comment: C: KEGGSOAP
... Hi Mark, I've added the function that a need to the package (in bold), as a copy of an existing function, bellow, in the KEGGSOAP.R, and then installed the function successfully, but I got this erro message, when I am installing or loading the package Note: Method with signature "PrimitiveSOAPType ...
written 7.5 years ago by Ricardo Silva110
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KEGGSOAP
... Hi, I would like to know if I can have access to zzz.R file of KEGGSOAP. best regards Ricardo ...
keggsoap written 7.5 years ago by Ricardo Silva110 • updated 7.5 years ago by Ricardo Silva20

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