User: Wenhu_Cao

gravatar for Wenhu_Cao
Wenhu_Cao70
Reputation:
70
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http://bioinfostar.com/
Last seen:
12 months ago
Joined:
3 years, 5 months ago
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Posts by Wenhu_Cao

<prev • 37 results • page 1 of 4 • next >
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multiple genome alignments with gene annotations
... Hi Folks, I am looking for some online tools with this function: multiple genome sequence alignment (eg. gb file), and also with gene annotations in the alignment results. Does anyone know such tools? Thanks! ...
genome annotation alignment written 12 months ago by Wenhu_Cao70
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Answer: A: GISTIC segment overlap error
... Thanks for the jet lag between me and most biostars, it gives me time to solve this problem by my own. The reason now seems trivial, however, I will note it for completeness. I substringed the first 12 chars of `Tumor-Sample-Barcode` to get patient only barcode for further analysis. The problem is ...
written 2.2 years ago by Wenhu_Cao70
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Comment: C: GISTIC segment overlap error
... I think I may find a possibl cause, which is collapsing barcode to patients (first 12 chars) would cause different sample types of the same patient to have only one name. I will try this idea and let you know the results. ...
written 2.2 years ago by Wenhu_Cao70
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GISTIC segment overlap error
... Hi everyone, I am a little confused about the error complained by GISTIC: GISTIC 2.0 input error detected: 169 segment overlaps detected in file '/path/***.seg.txt'. First overlap detected between segments at lines 26227 and 26377. I checked the first overlap lines in R, they are belo ...
gistic scna cnv snp written 2.2 years ago by Wenhu_Cao70 • updated 2.0 years ago by ysh0
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P-hacking or not in pan-cancer analysis
... Hi guys, I have read a few pan-cancer analysis papers, really big papers from CNS. Then, I am confused about the way what they are doing with the data. Normally, the data come from TCGA or other similar databases, these data are collected without any scientific hypothesis beforehand obviously, jus ...
p-value genome pan-cancer written 2.3 years ago by Wenhu_Cao70 • updated 3 months ago by Jean-Karim Heriche24k
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Comment: C: how to make this plot for mutation?
... Hi, I wonder if the maftools could make oncoplot including both scna and mutation data? Thx! ...
written 2.3 years ago by Wenhu_Cao70
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Comment: C: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Yeah, I also think so. ...
written 2.3 years ago by Wenhu_Cao70
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Comment: A: Where are mutation files (MAF) for TCGA normal samples on Firebrowse
... Have you known the differences between this two files yet? ...
written 2.3 years ago by Wenhu_Cao70
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Comment: C: Clinical Survival data of TCGA
... Although things have changed a lot now, but I do like the spirit of your script:) ...
written 2.3 years ago by Wenhu_Cao70
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Comment: C: Which Journals Should I Follow If I Write Software And Algorithms In Computation
... As a new fish, I did not find the place holding articles from the 3 conference, could you pls give a hint? ...
written 2.4 years ago by Wenhu_Cao70

Latest awards to Wenhu_Cao

Great Question 23 months ago, created a question with more than 5,000 views. For Error "Can't locate List/MoreUtils.pm in @INC"
Popular Question 23 months ago, created a question with more than 1,000 views. For Will the fastq-dump download the sra repetitively?
Popular Question 23 months ago, created a question with more than 1,000 views. For How does cBioPortal normalize data
Popular Question 23 months ago, created a question with more than 1,000 views. For Fundamental Analysis of TCGA RNA-seq Data-01
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Error "Can't locate List/MoreUtils.pm in @INC"
Popular Question 3.0 years ago, created a question with more than 1,000 views. For Error "Can't locate List/MoreUtils.pm in @INC"
Supporter 3.2 years ago, voted at least 25 times.

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