Bioconductor Motifs

Showing : motifs • reset

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1.9k

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genomation motifs

updated 9.5 years ago by altuna akalin ▴ 20 • written 9.5 years ago by sarah.blackstone7734 • 0

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illumina 450k motifs meme

10.1 years ago Gustavo Fernández Bayón ▴ 440

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1.4k

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MotifbreakR R motifs

6.8 years ago camerond • 0

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1.2k

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pwm motifs jaspar meme motif analysis

7.2 years ago rbronste ▴ 60

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1.1k

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motifs TF peakset plots

8.9 years ago rbronste ▴ 60

5 results • Page 1 of 1

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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…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Votes

Answer: Which preprocessing steps are needed before running limpa?

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

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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Scholar to Gordon Smyth 53k

Popular Question to Peter Hickey ▴ 760