Bioconductor Cuffdiff

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4.7k

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dexseq bitseq cuffdiff Differential exon usage isoforms

10.7 years ago • updated 10.6 years ago elle ▴ 10

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4.3k

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RNA-seq / XLOC cuffdiff

updated 4.1 years ago by Lan • 0 • written 5.7 years ago by mg.mahabad1365 • 0

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2.3k

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WGCNA cuffdiff

7.4 years ago sbbinfo90 • 0

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2.6k

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SpliceR Cuffdiff

updated 10.4 years ago by deppt002 • 0 • written 10.7 years ago by mfahim • 0

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4.5k

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htseqtools deseq2 counts cuffdiff

10.0 years ago Jon Bråte ▴ 270

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2.2k

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cummeRbund Script analysis RNAseq cuffdiff

updated 10.8 years ago by andrew.j.skelton73 ▴ 370 • written 10.8 years ago by mfahim • 0

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2.2k

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deseq2 cuffdiff

updated 10.7 years ago by Michael Love 43k • written 10.7 years ago by a.de-giorgio12 • 0

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1.9k

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deseq2 cuffdiff differential gene expression

10.6 years ago Assa Yeroslaviz ★ 1.5k

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2.0k

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GAGE Cuffdiff gene names

updated 10.2 years ago by Luo Weijun ★ 1.6k • written 10.2 years ago by user31888 ▴ 30

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1.8k

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cuffdiff sqlite

8.2 years ago handgabriel • 0

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1.7k

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kegg readcufflinks cuffdiff cuff

updated 8.2 years ago by thokall ▴ 160 • written 8.2 years ago by pierre.biojoux • 0

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705

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cummeRbund cufflink cuffdiff

updated 2.5 years ago by James W. MacDonald 68k • written 2.6 years ago by sumitra • 0

12 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: Subsetting data verses contrasts [DESeq2]?

A: WGCNA differences two groups 10 replicates each group

A: WGCNA sample size minimum: why?

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

Answer: Can you colour dendrogram branch clusters in pheatmap?

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Popular Question to Peter Hickey ▴ 760