User: Yuan Tian

gravatar for Yuan Tian
Yuan Tian110
Reputation:
110
Status:
Trusted
Location:
University College London
Last seen:
4 weeks ago
Joined:
1 year, 11 months 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 • 49 results • page 1 of 5 • next >
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Answer: A: cpg.annotate model requirements
... Hi, Kadm: Sorry that ChAMP did not designed parameter to set intercept in DMRcate, thus I suggest you directly run DMRcate package with specific settings. The result should not be too hard to organize. Best Yuan Tian ...
written 28 days ago by Yuan Tian110
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Answer: A: Differential Methylation Analysis using ChAMP
... Hi Zain: Sorry that I just see this post, you could also send email to champ450K@gmail.com. The error seems because of your beta matrix. I suspect after loading, the rowname of beta matrix would be read as first column. Could you post head(mydate) here as well? So after running champ.DMR(), you g ...
written 6 weeks ago by Yuan Tian110
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Comment: C: bumphunter stalls on "Smoothing coefficients"
... Sorry, I can't estimate it well, cause on my server and computer it works well...so I normally only use parallel settings. Best Yuan Tian rasmus.rydbirk [bioc] noreply@bioconductor.org 于 2019年5月20日周一 下午3:18写道: ...
written 3 months ago by Yuan Tian110
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Answer: A: bumphunter stalls on "Smoothing coefficients"
... Someone in my lab reported similar error before. But I can not replicate it on my server or laptop. So I eventually solved it by ask her setting cores=1, means not use parallel. Thus, I suspect the reason is doParallel package. Best Yuan Tian rasmus.rydbirk [bioc] noreply@bioconductor.org 于 2019年 ...
written 3 months ago by Yuan Tian110
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Answer: A: ChAMP::champ.norm Error in champ.BMIQ(beta[, x], design.v, sampleID = colnames(b
... Um...This is the second time I receive this error report this week. But I have never seen this error before, and no one reported before this week. I suspect the reason is some functions or packages ChAMP relies on are just updated, which caused some problem inside. I will have a look this week, and ...
written 3 months ago by Yuan Tian110
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Answer: A: New to bioinformatics
... Hi Kim: Thanks for the question. I personally think it's a very good question, to gather some useful resource for future new starters as well. I think [HarvardX Biomedical Data Science Open Online Training](http://rafalab.github.io/pages/harvardx.html) is good. Though I am too busy to finish them ...
written 4 months ago by Yuan Tian110
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Comment: C: clarification about bumphunter value output
... No, these are all values available. Beta value needs to be extracted yourself from origin beta matrix. ...
written 4 months ago by Yuan Tian110
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Answer: A: Loading packages in R minfi, limma
... Maybe you can try install 'bumphunter' package first, then rety minfi. Then you may get more specific error. Sometimes this error happens when some of your package failed to be installed, which might be trigger by missing library, env setting.e.g. ...
written 5 months ago by Yuan Tian110
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Answer: A: Reading 450k data in minfi
... Um...the error shows that the program can not infer slides and array information from your csv file, thus it may can not form correct "Basename" of IDAT file loading. So maybe you can paste part of your csv file here, I suspect the problem is missing or modified "Sentrix_ID" and "Sentrix_Position" ...
written 5 months ago by Yuan Tian110
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Comment: C: Error in Champ for Bioconductor analyzing Methlayion array data
... Um... Have you check if of the order of your beta matrix's column name is identical to your phone? And are you using public data set? for example GEO or TCGA? If so I may have a check on the data set as well. And you may email me to champ450K@gmail.com. ...
written 6 months ago by Yuan Tian110

Latest awards to Yuan Tian

Scholar 7 months ago, created an answer that has been accepted. For A: Error in Champ for Bioconductor analyzing Methlayion array data
Scholar 7 months ago, created an answer that has been accepted. For A: bumphunter stalls on "Smoothing coefficients"
Scholar 7 months ago, created an answer that has been accepted. For A: EPIC methylation array - analysis with ChAMP - how to export bed/wig file to vie
Autobiographer 21 months ago, has more than 80 characters in the information field of the user's profile.

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