User: sugus

gravatar for sugus
sugus30
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

<prev • 32 results • page 1 of 4 • next >
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Comment: C: Using Varscan without a matched normal
... Thank you, I just need to confirm this is worth trying. ...
written 1 day ago by sugus30
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Using Varscan without a matched normal
... 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 ...
varscan wes written 1 day ago by sugus30 • updated 1 day ago by Chris Miller21k
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How to determine subtype-specific mutations?
... 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. ...
exome-sequencing mutation subtypes written 3 days ago by sugus30
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Comment: C: How to remove batch effect in copy number segment mean
... Because it is a Pan Cancer analysis and it may have a batch effect. ...
written 8 months ago by sugus30
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How to remove batch effect in copy number segment mean
... 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- ...
cna segment combat batch effect written 8 months ago by sugus30 • updated 6 months ago by Biostar ♦♦ 20
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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 sugus30
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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 sugus30
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ANNOVAR annotate frameshift
... 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 ...
annovar mutation variant exonic written 9 months ago by sugus30
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extract gseaResult in clusterprofiler
... 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 ...
clusterprofiler gsea written 9 months ago by sugus30 • updated 9 months ago by Guangchuang Yu2.2k
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Comment: C: GSEA results change in clusterProfiler
... Actually nothing happened when I set logical seed. The results still change. ...
written 9 months ago by sugus30

Latest awards to sugus

Popular Question 5 months ago, created a question with more than 1,000 views. For customized clusterAlg of NMF in consensusClusterPlus
Popular Question 5 months ago, created a question with more than 1,000 views. For How to get a matrix gene weights in NMF
Popular Question 5 months ago, created a question with more than 1,000 views. For No result in enrichGO
Scholar 9 months ago, created an answer that has been accepted. For A: ANNOVAR annotate frameshift

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