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User: haiying.kong

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haiying.kong • 290
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290
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Location:
Germany
Last seen:
5 months ago
Joined:
4 years ago
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Posts by haiying.kong

<prev • 119 results • page 1 of 12 • next >
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KEGGREST -- gene list
... library(KEGGREST) > names(keggGet("map07049")[[1]]) [1] "ENTRY" "NAME" "PATHWAY_MAP" "COMPOUND" "REFERENCE" I need to get gene list (hugo-symbol) in each pathway. How can I get this from KEGGREST? > sessionInfo() R version 3.3.3 (2017-03-06) Platf ...
R keggrest bioconductor written 18 months ago by haiying.kong • 290 • updated 18 months ago by Damian Kao ♦ 15k
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Comment: C: Do structural variations on pseudo-gene mean any thing?
... Thank you very much for your reply. I have whole exome sequence data from matched blood and tumor samples, used Mirkat to identify somatic structural variations, then annotated them with gene names. ...
written 18 months ago by haiying.kong • 290
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Do structural variations on pseudo-gene mean any thing?
... I found structural variations from WES data. The top frequency genes are almost all pseudogenes. Could anyone please give me any advice? ...
biology written 18 months ago by haiying.kong • 290 • updated 18 months ago by d-cameron • 2.1k
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Comment: C: R survivalsvm package
... Not really. It is a general question about the software tool. For instance, if I run the example code on the manual of the software, the predicted values are: > pred.survsvm.reg$predicted [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [1,] 13.88731 14.94699 11.12112 ...
written 18 months ago by haiying.kong • 290
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R survivalsvm package
... Dear All, I am trying to use the R package: survivalsvm. I can get it running without error, survivalsvm and predict.survival, but if I look at the predicted values from the output of predict.survivalsvm, the values are not easy to interpret. They did not look like expected relapse time, or pro ...
R written 18 months ago by haiying.kong • 290
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Then, he will say: You are making excuse to be lazy! ...
written 20 months ago by haiying.kong • 290
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Thanks for the advice. If I run, there will be no driver genes identified. So nothing can be included in any paper that can be published. Just waste of my time. But I will keep the email anyway. ...
written 20 months ago by haiying.kong • 290
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Comment: C: I am asked to run MutSigCV on sample size 2!!!!!!
... Such communication is impossible with such dense head, sorry to say this word. After "because", there will be scientific explanation that involves statistics, and he refuses to hear any bioinformatics, or statistics, or mathematics in any occasion. He is 100000% pure biologist. ...
written 20 months ago by haiying.kong • 290
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Is epigenetic still hot field?
... It was very hot several years back. Is it still hot field? I feel much is done in this field, and nothing original is coming out. ...
epigenetic written 20 months ago by haiying.kong • 290 • updated 20 months ago by Devon Ryan ♦ 92k
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Comment: C: WES -- How come I found 40% mutations intron regions
... Thanks again for your help. It takes very very long to run MuTect even with many cores or nodes. So I do not have time to rerun, because I am trying to finish up soon. Is there any way to do the filtering from MuTect output? ...
written 21 months ago by haiying.kong • 290

Latest awards to haiying.kong

Epic Question 18 months ago, created a question with more than 10,000 views. For .dict file created by picard and by samtools
Popular Question 18 months ago, created a question with more than 1,000 views. For Can I use XHMM to detect somatic CNV?
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Popular Question 20 months ago, created a question with more than 1,000 views. For Average coverage for whole exome sequencing
Student 20 months ago, asked a question with at least 3 up-votes. For Somatic Mutation Identification without Paired Normal Sample
Great Question 21 months ago, created a question with more than 5,000 views. For .dict file created by picard and by samtools
Popular Question 21 months ago, created a question with more than 1,000 views. For BWA Suddenly says fail to open file
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