User: sugus
sugus • 30
- Reputation:
- 30
- Status:
- New User
- Location:
- China Pharmaceutical University
- Last seen:
- 1 day, 13 hours ago
- Joined:
- 2 years, 6 months ago
- Email:
- 6********@qq.com
Posts by sugus
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... Thank you, I just need to confirm this is worth trying. ...
written 1 day ago by
sugus • 30
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... Hi there,
I got an extremely incredible use of varscan.
You see, typically, we need a matched-normal sample as an input for varscan for somatic mutation calling.
However, if I used a matched-primary tumor as so-called normal baseline, and another matched-metastasis tumor sample, does it mean any ...
written 1 day ago by
sugus • 30
• updated
1 day ago by
Chris Miller ♦ 21k
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... Hi there,
We all know that given a profiling of gene expression data and two, maybe more, groups or subtypes, we could derive differentially expressed genes between these groups.
However, how to determine this kind of differential mutations or SNPs between groups by any stat-of-the-art methods.
...
written 3 days ago by
sugus • 30
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... Because it is a Pan Cancer analysis and it may have a batch effect. ...
written 8 months ago by
sugus • 30
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... Hi there,
I am wondering how to remove batch effect on segmented_scna data downloading from TCGA PANCANA project.
The demo of data format is as following:
Sample Chromosome Start End Num_Probes Segment_Mean
TCGA-KL-8323-11A-01D-2308-01 1 3218610 104558357 58272 0.0026
TCGA-KL-8323-11A- ...
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Comment:
C: ANNOVAR annotate frameshift
... Thank you for pointing this out but actually what's wrong is my input format.
I have solved this problem and attached the solution below.
Thanks again, Kevin. ...
written 9 months ago by
sugus • 30
1
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Answer:
A: ANNOVAR annotate frameshift
... I have solved this problem actually my input data format for ANNOVAR is wrong.
For those two insertion, it should change the end postion and the "-" to the following:
14 69257040 69257040 - GG
14 69257144 69257144 - CC
and if the mutation is a deletion, the end postion should correspond t ...
written 9 months ago by
sugus • 30
1
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1
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... Hi there,
I met a problem when annotate a nonframshift substitution but it was supposed to be frameshilt.
Here is the example of data (test.avinput) and code.
my data and the confusing annotations are the last two which I thought they were supposed to be frameshift.
14 69256505 69256505 G A
...
written 9 months ago by
sugus • 30
0
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1
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... Hi there,
My question is how to extract informtation of a specific pathway from gseaResult object derived from GSEA() in clusterProfiler R package.
Basicly, I can just use gesaplot to plot what I am interested in gseaResult, but I want to output a detailed information of this specific pathway. How ...
written 9 months ago by
sugus • 30
• updated
9 months ago by
Guangchuang Yu • 2.2k
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... Actually nothing happened when I set logical seed. The results still change. ...
written 9 months ago by
sugus • 30
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