Bioconductor Tcgautils

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TCGAutils

updated 13 months ago by James W. MacDonald 68k • written 13 months ago by xiaofeiwang18266 ▴ 60

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1.3k

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normalization RNASEQ Normalization TCGAutils TCGA

updated 3.2 years ago by ATpoint ★ 5.0k • written 3.2 years ago by Deniz • 0

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2.7k

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MultiAssayExperiment curatedTCGAData TCGAutils

5.2 years ago svlachavas ▴ 840

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1.8k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 5.2 years ago by Marcel Ramos 700 • written 5.2 years ago by svlachavas ▴ 840

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2.1k

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MultiAssayExperiment curatedTCGAData TCGAutils

updated 5.2 years ago by Marcel Ramos 700 • written 5.4 years ago by svlachavas ▴ 840

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6.0k

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TCGAutils TCGAbiolinks GenomicDataCommons

updated 6.6 years ago by Marcel Ramos 700 • written 6.6 years ago by Dario Strbenac ★ 1.6k

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1.3k

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TCGAutils

updated 6.9 years ago by Levi Waldron ★ 1.1k • written 6.9 years ago by vittorio.fortino • 0

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2.0k

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TCGAutils multiassayexperiment coad

updated 7.7 years ago by Marcel Ramos 700 • written 7.7 years ago by mario.zanfardino ▴ 160

8 results • Page 1 of 1

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Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Erik Wright ▴ 160

You are correct. Thank you for noticing some of this 'pollution' with "_2" suffixes was unnecessary. I posted an updated SILVA classifier …

Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0

Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Votes

A: The meaning of results produced by the bamQC function implemented in the ATACseq

The meaning of results produced by the bamQC function implemented in the ATACseqQC

A: Reference paper or resource for limma::diffSplice and edgeR::diffSpliceDGE metho

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

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