User: Yuan Tian

gravatar for Yuan Tian
Yuan Tian40
Reputation:
40
Status:
New User
Location:
Shanghai Institute for Biology Science, Shanghai, China
Website:
http://www.picb.ac.cn/...
Last seen:
6 hours ago
Joined:
9 months, 2 weeks ago
Email:
t**************@gmail.com

My name is Yuan Tian(田原), graduated from Harbin Institute of Technology(哈尔滨工业大学), Department of Computer Science. Now I am currently a PhD student in CAS-MAG Partner Institute of Computational Biology, which belongs to Shanghai Institute for Biology Science.

My research focus is DNA methylation, most specifically on illumina array data analysis. I currently published one paper on plos genetics and one paper on Bioinformatics. Also I designed and coded ChAMP along, maintaining it alone until now, which is not easy at all, but for me it's the best chance to get myself known and useful for labs outside China.

I like coding, and I think I have a creative mind. I am good at R, Node.js. Familiar with Python and C++. But to be honest, I think most  language are similar, I can pick them up in couple days, then  start to do real project, then learn more tricks in practices. I can code website front-end full stack, do data science work, create pipeline, research algorithm, make prototype for company e.g... basically every thing related to programming and science.

My English is OK I think, especially oral and listening, my spelling is not very good that's because Office can always remind me mistakes...

I have stayed nearly 27 years in China now, never been to any other countries before except UK (I get a very competitive government sponsorship for staying one year in UCL cancer institute, that's really fantastic memory, I really want to go back). 

I am about to graduate next year, and now looking for postdoc position. If you think I may contribute your lab work, you may contact me via email. I can maintain your server, help all coding work in your lab projects, and do independent research as well. 

^_^

Yuan Tian

Posts by Yuan Tian

<prev • 21 results • page 1 of 3 • next >
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Comment: C: install ChAMP under Ubuntu 18.04 in R 3.4.4 with error "maximal number of DLLs r
... Hello: This error used to appear on R version 3.4.X... The newest R version, say 3.5, should no longer have this problem. But I think what you are doing here is very much correct, setting R_MAX_NUM_DLLs is my way for these errors. But I always fix this by setting /etc file with sudo right. So I su ...
written 6 hours ago by Yuan Tian40
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Comment: C: QC and normalization of 450K data from CSVs instead of IDATs
... em...I see. Yes currently Functional Normalization indeed call for S4 object from minfi's reading function. I was thinking BMIQ solution. um...I can not see any easy solution now. Maybe some hacking on minfi's code work. Your data looks very much similar to a stage between IDAT file and RGChannalSe ...
written 10 days ago by Yuan Tian40
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Answer: A: QC and normalization of 450K data from CSVs instead of IDATs
... Hello Simone: I am not sure where did you get these three CSV, but ChAMP actually does NOT need any MythyLumiSet object, I am sure about that. All ChAMP function support solo beta matrix, and a list of phenotype, that's all. So I suspect you can directly modify your CSV file, extract beta matrix, I ...
written 10 days ago by Yuan Tian40
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Comment: C: Error when running ChAMP package
... Hello: Sorry that I was away to attend the examination in past 3 days. I think you may try champ.QC() directly, instead of champ.QC(myLoad). Because champ.QC() take beta matrix in myLoad object to do analysis, instead of myLoad object itself. Thus I suggest you try it. Or you may try: champ.QC(m ...
written 11 days ago by Yuan Tian40
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Comment: C: Error when running ChAMP package
... Hello: This error indicates you have put wrong type of parameter into champ.QC(). I suspect the parameter is "beta" in your question. Could you tell me what is your beta matrix looks like and how did you generated it? Best Yuan Tian ...
written 13 days ago by Yuan Tian40
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Answer: A: Beta-matrix - Differential methylation analysis
... Hello Dave: One of the feature for ChAMP is supporting beta-matrix for analysis instead of IDAT data. Because nearly all function in ChAMP are require pure matrix or data frame as input (parameter "beta" in functions). You just need to organize your data into a matrix or dataframe format, then put ...
written 10 weeks ago by Yuan Tian40
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Answer: A: ChAMP error while lazyloading the latest version ChAMP_2.9.10
...   Hello: The reason is R does not allow users to load more than 100 DLL. But some large packages like ChAMP would load many dependence, and these dependencies would also load many other packages. I am now fixing this issue, but it's really challenging because I need to decrease some relying packa ...
written 10 weeks ago by Yuan Tian40
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Answer: A: "Seems your IDAT file not from one Array"
... Hello David: Even EPIC array have different versions. For example, on Illumina website, you could find various versions of EPIC manifests. Version 2 have different number of CpG covered with version 4 if I remember correctly. Different versions of EPIC data would have slightly differences on CpG c ...
written 10 weeks ago by Yuan Tian40
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Answer: A: ChAMP was installed and library in R, however, I can't use the function
... Hello: The reason is R does not allow users to load more than 100 DLL. large packages like ChAMP would load many dependence packages, and these dependences would also load many other packages. I am now fixing this issue, but it's challenging because I need to decrease some relying packages maybe.  ...
written 11 weeks ago by Yuan Tian40
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Comment: C: could not find function "champ.load"
... Hello David: You can reset your Renviron file and add one line: R_MAX_NUM_DLLS=512, then this error should be no more. The Renviron file should be at /usr/local/lib64/R/3.4.4/lib64/R/etc (on my computer). I am now fixing the package, deciding to cut down some packages. I have detected that if I r ...
written 12 weeks ago by Yuan Tian40

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