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User: pj dias

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pj dias60
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Posts by pj dias

<prev • 10 results • page 1 of 1 • next >
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Answer: A: BSGenome problem with forgeBSgenomeDataPkg command
... Hi Hervé, I upgraded R and bioconductor, and the problem resided in the species field have been changed to common_name field. With this small correction, the genome forging went OK. Maybe could be a thing to add to the text of the pdf file "How to forge a BSgenome data package", remarking that m ...
written 2.6 years ago by pj dias60
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latest R version compatible with BSgenome
... Hi, I'm writing just to ask if someone knows the latest version of R compatible with BSgenome. When I try to install the latest available version of R, version 3.3.1, i get: package ‘BSgenome’ is not available (for R version 3.3.1) (the same with GenomicFeatures, and probably related genome mani ...
bsgenome written 2.6 years ago by pj dias60 • updated 2.6 years ago by Martin Morgan ♦♦ 22k
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Comment: C: BSGenome problem with forgeBSgenomeDataPkg command
... Hi Hervé, Thanks for the quick reply. I upgraded R and Bioconductor to the latest release, in case of R is 3.3.1. However, when I tried to install BSgenome I got the error Warning message: package ‘BSgenome’ is not available (for R version 3.3.1) Can someone tell me what is the latest R versio ...
written 2.6 years ago by pj dias60
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BSGenome problem with forgeBSgenomeDataPkg command
... Hi to the Bioconductor community, I have been in the process of forging many genomes and found that after the upgrade of R to a version like R version 3.2.3 (2015-12-10), the use of the forgeBSgenomeDataPkg command originates a error that does not occur when I use a R version like R version 3.0.2 ( ...
bsgenome forge written 2.6 years ago by pj dias60
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Answer: A: Genes and Metabolites
... Hi. N.O. In my opinion, the best suitable tool for that objective is a network exploration software like cytoscape. 1) Install cytoscape version 2.8.3, and add the toolbox cySBML. 2) Obtain the SBML file for the metabolic reconstruction of the organism you are studying 3) search your metabolite, ...
written 5.4 years ago by pj dias60
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Answer: A: pathview puzzle
... Hi Weijun, Interesting tool pathview, is there any plans to extend its capabilities I/O to handle SBML files? People from metabolic modelling would probably benefit a lot from that extension, and SBML is more or less the reference input file in pathway/metabolic analysis. Regards, Pj 2013/9/3 ...
written 5.5 years ago by pj dias60
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Comment: C: Motif search -- access to JASPAR, MotIV package, more TF-PWM relationships?
... Regarding S. cerevisiae, there is a great resource, YEASTRACT database ( http://www.yeastract.com/). It compiles the motifs already identified, documented regulation based on wet-lab research and potential regulation based on comparison of motifs against the promoter region of genes. It is revi ...
written 6.8 years ago by pj dias60
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Introduction to the rsbml functionalities
... I have also just beginning to use rsbml. Is there a more detailed introduction to the package functionalities? If not, a few code examples demonstrating the potential of the package would be very useful. Pj [[alternative HTML version deleted]] ...
rsbml written 8.3 years ago by pj dias60 • updated 8.3 years ago by Michael Lawrence10k
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Comment: C: Anyone thinking of expanding rsbml capability of reading SBML versions?
... You are right, I have mistaken with Cytoscape SBML import capabilities, but in fact my problem is with a SBML file level=2, version=4 ( http://www.comp-sys-bio.org/yeastnet/) (that’s why I couldn’t import it to rsbml). Hope next augmentation of rsbml SBML import capability will occur soon, so this p ...
written 8.3 years ago by pj dias60
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Anyone thinking of expanding rsbml capability of reading SBML versions?
... Hi, I'm a new user of bioconductor and I'm starting to work with rsbml package. The problem is that this package only recognizes currently level=2, version=1, so I'm sending this message if there is any possibility to import to R SBML files with higher versions. Pj [[alternative HTML versi ...
written 8.3 years ago by pj dias60 • updated 8.3 years ago by Michael Lawrence10k

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