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:
3 weeks, 3 days ago
Joined:
1 year 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 • 27 results • page 1 of 3 • next >
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Comment: C: Taking relatedness among individuals into account in differential methylation an
... Um...Sorry that I think ChAMP cannot incorporate relatedness matrix, I have never done project involved with that, thus I did not develop this functionality in ChAMP. Maybe you can consider minfi? Best Yuan Tian  ...
written 4 weeks ago by Yuan Tian40
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Answer: A: DNA methylation analysis without raw data IDAT files
... Actually ChAMP can do analysis with simple beta matrix and pheno vector, it's not relying on IDAT file. So if you can extract beta information from your file into proper matrix, you can then use ChAMP for all following analysis. But ChAMP does not provide loading function from your file format to R ...
written 4 weeks ago by Yuan Tian40
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Comment: C: Error biocLite() newest version of ChAMP
... Hello: Based on my experience, I don't this is a problem with ChAMP, but could be some error related to R environment. I just tried to install ChAMP on R 3.5.1 and it works. Could you try R 3.5.1, because R 3.3.1 is a little bit too old. Best Yuan Tian ...
written 4 weeks ago by Yuan Tian40
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Comment: C: champ.runCombat is failing: "invalid 'row.names' length"
... By the way, could you please check if the batch varaible (say Slides) in your pd is "Character" or "Factor" format? I found that some users' "Slides" column is numeric, which might triggle this error. To check the format, use code: class(pd[,X]). If it's numeric, to change the format, use code: pd ...
written 6 weeks ago by Yuan Tian40
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Comment: C: champ.runCombat is failing: "invalid 'row.names' length"
... Hello: Could you show send your pd file (Sample_Sheet.csv) to me to check what's wrong with it? To email champ450K@gmail.com. Best Yuan Tian ...
written 6 weeks ago by Yuan Tian40
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Comment: C: Help with Errors in DMRcate ChAMP package
... Hello: The program failed at the very begining step: Mapping CpGs to annotation, thus I am a little bit suspect the problem is your beta matrix. Could your please check if your beta matrix : hs850kBetaMatrix, contains valid CpG rownnames? Say using code: hs850kBetaMatrix[1:5,1:5] in R to check? B ...
written 7 weeks ago by Yuan Tian40
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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 3 months 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 3 months 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 3 months 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 3 months ago by Yuan Tian40

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