Bioconductor StageR

Showing : stageR • reset

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2.3k

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DESeq2 stageR

19 months ago alephreish • 0

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902

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DEXSeq stageR

2.3 years ago jbono ▴ 10

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1.0k

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stageR

updated 4.3 years ago by Koen Van den Berge ▴ 180 • written 4.4 years ago by giwa.ao • 0

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1.4k

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DRIMSeq stageR

updated 6.9 years ago by Koen Van den Berge ▴ 180 • written 6.9 years ago by sdvie • 0

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2.3k

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stageR rnaseqDTU DRIMSeq DEXSeq

7.0 years ago d-joester ▴ 20

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1.9k

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limma stageR decideTests

updated 7.1 years ago by Koen Van den Berge ▴ 180 • written 7.1 years ago by maltethodberg ▴ 180

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1.7k

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drimseq rnaseqdtu stager

updated 7.2 years ago by Michael Love 43k • written 7.2 years ago by Jack.Hearn • 0

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2.3k

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DEXSeq StageR rnaseqDTU

updated 7.3 years ago by Michael Love 43k • written 7.3 years ago by rbenel ▴ 50

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2.8k

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drimseq stageR dtu salmon rna seq

updated 7.6 years ago by Koen Van den Berge ▴ 180 • written 7.6 years ago by fiona.dick91 ▴ 60

9 results • Page 1 of 1

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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?

Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2 by colinmccornack • 0

FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…

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?

Awards • All

Scholar to Gordon Smyth 53k

Popular Question to Peter Hickey ▴ 760