User: Zhang, Jitao David

Reputation:
100
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Location:
Switzerland
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Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
4 years, 8 months ago
Email:
j****************@roche.com

Computational biologist working at Roche Innovation Center Basel, F. Hoffmann-La Roche.

Interested in applying statistical and machine learning methods for disease understanding and drug development.

Posts by Zhang, Jitao David

<prev • 19 results • page 1 of 2 • next >
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Answer: A: possible bug in parseKGML?
... Dear Martin,    Do I get you correctly that you raised two questions?    The first question is about the bidirectionality. Currently it is not supported, namely only the relation from node 47 to node 53 is parsed. The reason is that I believe (though I may be wrong!) when I looked it a few years a ...
written 5 weeks ago by Zhang, Jitao David100
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Comment: C: ddCT Package for StepOnePlus qPCR output
... Dear rbronste, not yet. I will try to catch up next week. Best wishes, David On Wed, Aug 2, 2017 at 5:57 PM, rbronste [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User rbronste <https: support.bioconductor.org="" ...
written 10 weeks ago by Zhang, Jitao David100
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Answer: A: ddCT Package for StepOnePlus qPCR output
... Dear Rob, do you mind providing an example? Thanks, David ...
written 11 weeks ago by Zhang, Jitao David100
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Answer: A: Recent build and parsing error in pathview
... Dear all,     Thanks for the report. In the latest versions (devel 1.37.2/release 1.38.1) I have exported required functions to make the example work. Please let me know if there are still problems.     Best, Jitao David Zhang, the author of KEGGgraph     ...
written 11 weeks ago by Zhang, Jitao David100
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Answer: A: incorrect direction in compound-gene interactions
... Dear Andrea, Thanks for the report of the interesting observation. I think in the KGML definition, an interaction should be of the direction from 'entry1' to 'entry2' <http: www.kegg.jp="" kegg="" xml="" docs=""/>, which would translate into "hsa:5581"--> "cpd:C00031". But indeed a ...
written 3 months ago by Zhang, Jitao David100
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Comment: C: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, I looked into the issue and confirm that it's observed in R 3.4 but not in older versions. In case anyone is interested in the cause: the warning is caused by XML::xmlChildren.xmlNode, which tries to build a structure out of NULL in case there's no children of a given XML node. ...
written 3 months ago by Zhang, Jitao David100
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Comment: C: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, Would you mind providing me the information of sessionInfo()? Because I cannot replicate the findings on my machine, i.e. I did not receive the warnings. My sessionInfo() is as follows: R version 3.3.2 (2016-10-31) > Platform: i686-pc-linux-gnu (32-bit) > Running under: L ...
written 4 months ago by Zhang, Jitao David100
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Answer: A: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, I will have a look. This should not affect the functionality of the package, though. Best wishes, David On Thu, Jun 8, 2017 at 11:00 AM, AR3513 [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are following on support.bioconductor.org > > User A ...
written 4 months ago by Zhang, Jitao David100
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Answer: A: retrieve human readable gene names from KEGG identifiers
... I am glad that you digged out translateKEGGID2GeneID:) Have fun, David ...
written 20 months ago by Zhang, Jitao David100
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Answer: A: retrieve human readable gene names from KEGG identifiers
... Dear Osvaldo,    Thank you for using KEGGgraph.    The identifier (mmu:12801) is composed of species (mmu) and Entrez Gene ID (12801). So strsplit will do the trick to get EntrezGeneID    From GeneID to gene symbos one can choose many ways. One of them is biomaRt.     Best wishes, David ...
written 20 months ago by Zhang, Jitao David100

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