User: Researcher

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Researcher10
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Posts by Researcher

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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... Yes I used TCGAbiolinks and it worked for me. Thanks ...
written 5 days ago by Researcher10
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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... I found this very helpful. http://bioinformaticsfmrp.github.io/TCGAbiolinks/subtypes.html Thanks ...
written 5 days ago by Researcher10
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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... 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 Researcher10
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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... Can you please help.....? I really got stuck. Any help would be appreciated. Thanks. ...
written 5 days ago by Researcher10
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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... 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 Researcher10 • updated 5 days ago by Kevin Blighe37k
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Comment: C: Finding Mutation status of IDH1 from FireBrowse data
... 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 Researcher10
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Comment: A: Survival analysis with gene expression
... 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 Researcher10
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Comment: C: Integrating methylation in survival analysis
... But would averaging the beta values be recommended, can't we consider the continuous values for each probe? ...
written 8 days ago by Researcher10

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