User: gabriele.sales

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Posts by gabriele.sales

<prev • 8 results • page 1 of 1 • next >
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Answer: A: Error installing graphite
... Dear Lluís, I've been able to reproduce the issue you mentioned on a 32 bit system. I developed a fix; it is already available in the development version of graphite (http://bioconductor.org/packages/3.9/bioc/html/graphite.html). I will also backport the change to the stable release. It should be ...
written 12 months ago by gabriele.sales100
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Comment: C: graphite and PoTRa
... Dear user, I don't think devtools are really needed here. Why don't you use the following? library(graphite) humanReactome <- pathways("hsapiens", "reactome") You can then obtain other species / databases calling the pathways function again, with different arguments. Have a look at pathwayDat ...
written 20 months ago by gabriele.sales100
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Answer: A: graphite and PoTRa
... Dear user, I'm one of the authors of the graphite package. The error you report depends on the fact that the example rdata provided on the PoTRA homepage erroneously includes an old copy of graphite pathways (object humanKEGG), instead of retrieving them from the package itself. The internal struct ...
written 21 months ago by gabriele.sales100
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Comment: C: Indirect path in KEGG, activation or inhibition?
... We will release a new version of graphite with the next Bioconductor release, which should take place mid-April.   Best,   Gabriele   ...
written 2.8 years ago by gabriele.sales100
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Answer: A: Indirect path in KEGG, activation or inhibition?
... Dear Haoran, this is a good observation. Right now graphite is not able to reconstruct the "sign" of the reaction when it goes through a compound, like PIP3 here. It would be nice to do that, however. We'll try to implement this behaviour in a new release.   Best,   Enrica & Gabriele ...
written 2.8 years ago by gabriele.sales100
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Answer: A: KEGG data error?
... Dear Haoran, graphite developers here. We have checked the conversion of the pathway you mention. In the first case (repression from FOXO to CCND1), the KGML file corresponding to the pathway doesn't include such reaction. We have already observed a number of cases in which the graphical plot does ...
written 2.8 years ago by gabriele.sales100
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Answer: A: Reactome pathways in ReactomeDB/graphite
... Dear User, graphite developers here. We've taken a look at the "HDL-mediated lipid transport" pathway, and in particular at the ALB protein (P02768). In the original Reactome pathway such protein takes part to the following biochemical reaction: ALB + 1-acyl LPC -> Complex(ALB + 1-acyl LPC) ...
written 2.9 years ago by gabriele.sales100
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Answer: A: graphite KEGG pathway list vs KEGG pathway list
... There are a number of reasons why a KEGG pathway could be missing from graphite. First of all, take as an example hsa00514 (Other types of O-glycan biosynthesis). The corresponding KGML file does not contain any "relation" or "reaction", so graphite cannot extract any meaningful edge. As a result, ...
written 4.7 years ago by gabriele.sales100

Latest awards to gabriele.sales

Scholar 20 months ago, created an answer that has been accepted. For A: Reactome pathways in ReactomeDB/graphite
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Reactome pathways in ReactomeDB/graphite
Scholar 4.7 years ago, created an answer that has been accepted. For A: Reactome pathways in ReactomeDB/graphite
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: Reactome pathways in ReactomeDB/graphite

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