User: sedaghat.nafiseh

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Posts by sedaghat.nafiseh

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Comment: C: A question about rBiopaxParser
... Yes, you're right. It is because of nested pathways. Thanks for introducing the 'paxtoolsr'. It is helpful. ...
written 4.4 years ago by sedaghat.nafiseh20
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Comment: C: How can I find the relation between pathways in KEGG?
... Thank you so much for your kindness. One more question: Do you know how can I find such relations in other pathway database, such as reactome? They code pathways as biopax files. ...
written 4.4 years ago by sedaghat.nafiseh20
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Comment: C: How can I find the relation between pathways in KEGG?
... I think they show some effects, say regulation, between complexes in pathways. I have not found any explicit definition for them, yet. ...
written 4.4 years ago by sedaghat.nafiseh20
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Comment: C: How can I find the relation between pathways in KEGG?
... In kegg maps, there are some arrows from one pathway to another pathway; I'd like to find them for each pair of pathways. ...
written 4.4 years ago by sedaghat.nafiseh20
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Answer: A: aracne in R using minet package
... You can see a sample code as below: 'data' is a matrix which each row corresponds to a prob and each column corresponds to gene. mim <- build.mim(data,estimator="spearman") net1 <- aracne(mim,eps=0.1)   ...
written 4.4 years ago by sedaghat.nafiseh20
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How can I find the relation between pathways in KEGG?
... How can I find the relation between pairs of pathways in pathway databases like KEGG? Is there any R-package to do this? ...
pathway R kegg written 4.4 years ago by sedaghat.nafiseh20 • updated 4.4 years ago by Pavel Senin1.9k
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Answer: A: KEGG pathways associated to a gene using BiomaRt
... You can use 'graphite' R-package. ...
written 4.4 years ago by sedaghat.nafiseh20
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Answer: A: KEGG cancer pathways
... Hello Amy, I think the easiest way is using R-packages. You can retrieve the name of genes in pathways through 'graphite' package. Nafiseh ...
written 4.4 years ago by sedaghat.nafiseh20
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A question about rBiopaxParser
... Hi all, Who knows what is the difference between the outputs of 'listPathwayComponents' and 'pathway2Geneset' in rBiopaxParser? It seems that the 'listPathwayComponents' returns all interactions which are available in the corresponding pathway and 'pathwayGeneset' returns physical entities and 'Bi ...
pathway rbiopaxparser biopax R written 4.4 years ago by sedaghat.nafiseh20 • updated 4.4 years ago by emekdemir100

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