Bioconductor Cuffdiff

Showing : Cuffdiff • reset

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476

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cummeRbund cufflink cuffdiff

updated 15 months ago by James W. MacDonald 67k • written 16 months ago by sumitra • 0

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3.4k

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RNA-seq / XLOC cuffdiff

updated 2.8 years ago by Lan • 0 • written 4.5 years ago by mg.mahabad1365 • 0

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1.7k

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WGCNA cuffdiff

6.2 years ago sbbinfo90 • 0

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1.4k

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cuffdiff sqlite

7.0 years ago handgabriel • 0

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1.4k

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kegg readcufflinks cuffdiff cuff

updated 7.0 years ago by thokall ▴ 160 • written 7.0 years ago by pierre.biojoux • 0

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3.7k

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htseqtools deseq2 counts cuffdiff

8.8 years ago Jon Bråte ▴ 260

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1.7k

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GAGE Cuffdiff gene names

updated 9.0 years ago by Luo Weijun ★ 1.6k • written 9.0 years ago by user31888 ▴ 30

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2.2k

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SpliceR Cuffdiff

updated 9.2 years ago by deppt002 • 0 • written 9.4 years ago by mfahim • 0

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1.5k

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deseq2 cuffdiff differential gene expression

9.4 years ago Assa Yeroslaviz ★ 1.5k

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3.6k

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dexseq bitseq cuffdiff Differential exon usage isoforms

9.5 years ago • updated 9.4 years ago elle ▴ 10

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1.8k

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deseq2 cuffdiff

updated 9.5 years ago by Michael Love 42k • written 9.5 years ago by a.de-giorgio12 • 0

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1.9k

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cummeRbund Script analysis RNAseq cuffdiff

updated 9.6 years ago by andrew.j.skelton73 ▴ 370 • written 9.6 years ago by mfahim • 0

12 results • Page 1 of 1

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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