User: haiying.kong
haiying.kong • 230
- Reputation:
- 230
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- Germany
- Last seen:
- 11 months, 3 weeks ago
- Joined:
- 3 years, 6 months ago
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Posts by haiying.kong
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... 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 ...
written 11 months ago by
haiying.kong • 230
• updated
11 months ago by
Damian Kao ♦ 15k
0
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2
answers
407
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2
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... 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 12 months ago by
haiying.kong • 230
3
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2
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407
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6 follow
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... I found structural variations from WES data. The top frequency genes are almost all pseudogenes.
Could anyone please give me any advice? ...
written 12 months ago by
haiying.kong • 230
• updated
12 months ago by
d-cameron • 2.0k
0
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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 12 months ago by
haiying.kong • 230
0
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0
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323
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... 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 ...
written 12 months ago by
haiying.kong • 230
0
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2
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141
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2
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... Then, he will say:
You are making excuse to be lazy! ...
written 13 months ago by
haiying.kong • 230
0
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2
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141
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2
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... 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 13 months ago by
haiying.kong • 230
0
votes
2
answers
141
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2
answers
... 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 13 months ago by
haiying.kong • 230
1
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1
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304
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1
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... 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. ...
written 14 months ago by
haiying.kong • 230
• updated
14 months ago by
Devon Ryan ♦ 88k
0
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1
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1.0k
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1
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... 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 15 months ago by
haiying.kong • 230
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