Showing : GDCprepare • reset
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GDCprepare error in TCGAbiolinks
tcgabiolinks gdcprepare differential expression
23 months ago fawazfebin ▴ 30
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GDCprepare - error
TCGABiolinks GDCprepare
2.2 years ago vm • 0
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TCGAbiolinks GDCprepare error
TCGAbiolinks GDCprepare error
updated 2.2 years ago by ▴ 150 • written 2.2 years ago by ▴ 10
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Issue with TCGAbiolinks package.
TCGA GDCprepare
2.6 years ago salvocomplicazioni1 • 0
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705
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GDCprepare stop working for some unknown reason
tcgabiolinks gdcprepare
updated 2.8 years ago by 58k • written 2.8 years ago by • 0
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Reasoning for illegal operation
tcgabiolinks illegaloperation gdcprepare
3.8 years ago lisa8191 • 0
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How to get treatment information with TCGAbiolinks?
gdcprepare tcgabiolinks treatment_type R data extraction
updated 4.2 years ago by ★ 1.5k • written 4.3 years ago by • 0
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TCGA controlled data
R tcgabiolinks gdcprepare
4.3 years ago ugandhar.ch1 • 0
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Extract gene expression values from GDCprepare object
tcgabiolinks tcga tcgadownload gdcprepare gdc
updated 4.5 years ago by ▴ 260 • written 4.6 years ago by • 0
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TCGAbiolinks GDCprepare fails to connect to Biomart web server
tcgabiolinks gdcprepare
5.0 years ago sabarinath.chandrasekharan ▴ 10
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Error during GDCprepare
tcgabiolinks gdcprepare
updated 5.0 years ago by ▴ 150 • written 5.0 years ago by ▴ 10
11 results • Page 1 of 1
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Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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Scholar to James W. MacDonald 58k
Teacher to Michael Love 34k
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