User: Yuan Tian

gravatar for Yuan Tian
Yuan Tian0
Reputation:
0
Status:
New User
Location:
Shanghai Institute for Biology Science, Shanghai, China
Website:
http://www.picb.ac.cn/...
Last seen:
3 weeks, 2 days ago
Joined:
5 months, 3 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 • 8 results • page 1 of 1 • next >
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Answer: A: ChAMP Methylation analysis error code "could not find function champ.load"
... Hello: It seems like you failed to load ChAMP. Based on your error message, I think maybe you can try install digest and bumphunter package, then load ChAMP again. Normally it should be installed along with ChAMP, but it worth trying. Best Yuan Tian ...
written 25 days ago by Yuan Tian0
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Answer: A: error when using M-values in ChAMP
... Hello: I suspect you did not extract M value correctly because the error shows ncol(beta) is 0, which means you did not input a matrix. I suspect you used myLoad$beta (which is champ's default setting), but M matrix could be in myLoad$M. Best Yuan Tian ...
written 4 weeks ago by Yuan Tian0
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Comment: C: Error code using ChAMP/Bioconductor, unable to load data from EPIC methylation a
... Hello: I suspect something wrong with your Sample_Sheet.csv file. Could you sent it to champ450K@gmail.com for me to check? I suspect your basename is duplicated, which means champ can not extract name for your IDAT data. Best Yuan Tian ...
written 4 weeks ago by Yuan Tian0
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Comment: C: Errors with champ.block
... Hello Amit: DMR.GUI() would firstly calculate significant DMPS then map them back to DMRs, so after calculating DMP, there is a process mapping DMPs back to DMRs, in my memory, it would take some longer time. Have you try my Demo data? If Demo Data works, I think there is no problem with function. ...
written 10 weeks ago by Yuan Tian0
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Answer: A: Errors with champ.block
... Hello Amit: Could you provide two things: one is sessionInfo, I want to know which version of ChAMP you are using, and secondly, could you paste more information here? I remember all champ function should return many messages, by providing them I could locate problem faster. Best Yuan Tian ...
written 10 weeks ago by Yuan Tian0
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Comment: C: champ.DMP phenotypes and covariates
... Hello Olga: The "deconvoluted components" means latent variable which could explain variance in your original data set. For example, SVD is a commonly used deconvolution method for matrix data. You may read something related to SVD or PCA (principle component analysis). In short, we take original d ...
written 3 months ago by Yuan Tian0
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Answer: A: champ.DMP phenotypes and covariates
... Hello Olga: Based on your description, I think you are actually doing paired analysis, means you actually have paired data, see if some treatment could have effect on then. champ.DMP() is NOT designed for this analysis, nor do champ.DMR(), champ.DMB() designed for them. Please don't use them for t ...
written 3 months ago by Yuan Tian0
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Answer: A: error with champ.load
... Hello Olga: Firstly, champ.QC() failed because of lacing of Sample_Group column, which could because your csv file does not contain Sample_Group. That's OK because different research have different column name on most interested covariates. In champ.QC() there should be a parameter called "pheno", ...
written 3 months ago by Yuan Tian0

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