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User: Timze W

gravatar for Timze W
Timze W • 20
Reputation:
20
Status:
New User
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Last seen:
2 months, 2 weeks ago
Joined:
11 months ago
Email:
w******@gmail.com

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Posts by Timze W

<prev • 5 results • page 1 of 1 • next >
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Comment: C: Are there any way to find DMR with the data in TCGA methylation level3?
... Thanks for your help. I have finally solved this problem, but what I use is the other tool called ChAMP., it can accept the beta value matrix as input. AND for the TCGAbiolinks, I have noticed it have this function, but when I read its code in GitHub, it seems do the same works for DMRs just as fo ...
written 3 months ago by Timze W • 20
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should FASTA files be sorted before indexed with SAMtools?
... Hello dears, We can index the files to access random sequences fast, and it should be sorted before indexed for the SAM/BAM. But when it turns to FASTA files, I could not understand why we can directly index without sort first ? samtools faidx Are there any easy explanation? THANKS ...
fasta sort samtools index written 4 months ago by Timze W • 20 • updated 4 months ago by finswimmer ♦ 9.9k
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Are there any way to find DMR with the data in TCGA methylation level3?
... Hi dear all, after downloaded the illumina 450K methylation chip data from TCGA, I have identified the DMCs with Fisher test for each probe, but I have no idea to identify the **DMRs**. For example I wanna find out the different methy- regions with 1Kb long. Any tool can do it directly? Could any ...
450k tcga methylation dmr written 5 months ago by Timze W • 20 • updated 3 months ago by Kevin Blighe ♦ 37k
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Comment: C: Some symbols share the same ensembl ID in org.Hs.eg.db but not in ensembl websit
... I will update this post as soon as there is new progress. ...
written 11 months ago by Timze W • 20
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Some symbols share the same ensembl ID in org.Hs.eg.db but not in ensembl website, how to deal with it?
... Hello, as a newbie, I do get some troubles in converting ensembl ID to gene SYMBOL. For example, when I convert the "ENSG00000158164" to SYMBOL in the R library "org.Hs.eg.db", it has 2 symbol names. This is my code and output: > select(org.Hs.eg.db, keys="ENSG00000158164",columns=c("CHR" ...
org.hs.eg.db gene symbol ensembl written 11 months ago by Timze W • 20

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