User: Zhang, Jitao David

Reputation:
90
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Location:
Switzerland
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Google Scholar Page
Last seen:
3 days, 22 hours ago
Joined:
4 years, 6 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 • 18 results • page 1 of 2 • next >
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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 15 days ago by Zhang, Jitao David90
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Answer: A: ddCT Package for StepOnePlus qPCR output
... Dear Rob, do you mind providing an example? Thanks, David ...
written 22 days ago by Zhang, Jitao David90
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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 24 days ago by Zhang, Jitao David90
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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 5 weeks ago by Zhang, Jitao David90
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Comment: C: KEGGgraph warning: "In structure(x$children, class = "XMLNodeList") :"
... Dear Andrea, I looked into the issue and confirm that it's observed in R 3.4 but not in older versions. In case anyone is interested in the cause: the warning is caused by XML::xmlChildren.xmlNode, which tries to build a structure out of NULL in case there's no children of a given XML node. ...
written 8 weeks ago by Zhang, Jitao David90
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Comment: C: KEGGgraph warning: "In structure(x$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 8 weeks ago by Zhang, Jitao David90
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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 10 weeks ago by Zhang, Jitao David90
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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 18 months ago by Zhang, Jitao David90
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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 18 months ago by Zhang, Jitao David90
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Answer: A: ddCt calculation using bioconductor package
... Dear gv,    From version 1.24.0, it's possible to use a data.frame as input. Check 'example(InputFrame)' out.    Otherwise it's also possible to write a specific parser of eds files. Do you mind sharing an example with me? That can be quite helpful since I do not have access to such files.     If ...
written 2.2 years ago by Zhang, Jitao David90

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