User: Researcher
Researcher • 10
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Posts by Researcher
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... Yes I used TCGAbiolinks and it worked for me.
Thanks ...
written 5 days ago by
Researcher • 10
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... I found this very helpful.
http://bioinformaticsfmrp.github.io/TCGAbiolinks/subtypes.html
Thanks ...
written 5 days ago by
Researcher • 10
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... I want to find all those LGG samples who have IDH gene mutation. Isn't it the correct way to do this? Can you please suggest any alternative method for the same.
Thanks ...
written 5 days ago by
Researcher • 10
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... Can you please help.....?
I really got stuck.
Any help would be appreciated.
Thanks. ...
written 5 days ago by
Researcher • 10
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... Sure, here it is with the error it got.
[bm@cn4262 LGG]$ wget http://firebrowse.org/api/v1/Analyses/Mutation/MAF?format=tsv&cohort=LGG&tool=MutSig2CV&gene=IDH1&page=1&page_size=250&sort_by=cohort
[1] 37587
[2] 37588
[3] 37589
[4] 37590
[5] ...
written 5 days ago by
Researcher • 10
• updated
5 days ago by
Kevin Blighe ♦ 37k
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... Hi,
I tried to follow your instructions to get the Url for LGG samples having IDH1 mutation. But the URL didn't work when I copied this to my console with wget. Am I doing this correct or there is some other way of downloading this?
Looking forward to your reply.
Thanks ...
written 6 days ago by
Researcher • 10
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... Hi Kevin,
I am curious to ask can we use Beta values for methylation from each probe instead of the read-count from gene expression.
If yes, these values are continuous and range from 0 to 1, would it be recommended to convert these also to Z score. ...
written 8 days ago by
Researcher • 10
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... But would averaging the beta values be recommended, can't we consider the continuous values for each probe? ...
written 8 days ago by
Researcher • 10
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