Bioconductor Wgcna package

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wgcna WGCNA wgcna package

4.8 years ago coyoung ▴ 10

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wgcna wgcna package modulepreservation

updated 6.0 years ago by Peter Langfelder ★ 3.0k • written 6.0 years ago by bekah ▴ 40

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wgcna wgcna package

6.0 years ago Jack • 0

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wgcna package wgcna

6.0 years ago anni.djurhuus • 0

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wgcna package TCGA LocusLinkID genecode ensembl

updated 6.1 years ago by James W. MacDonald 67k • written 6.1 years ago by modarzi ▴ 10

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wgcna package software error

updated 6.1 years ago by Peter Langfelder ★ 3.0k • written 6.1 years ago by giuseppe0525 • 0

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wgcna wgcna package consensus

6.2 years ago 2323982403 ▴ 60

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wgcna wgcna package

6.2 years ago antoinefelden ▴ 10

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WGCNA wgcna package

updated 6.3 years ago by Peter Langfelder ★ 3.0k • written 6.3 years ago by bdy8 ▴ 10

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wgcna wgcna package

6.3 years ago 2323982403 ▴ 60

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WGCNA wgcna package wgcna bicor

6.3 years ago bekah ▴ 40

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wgcna package

updated 6.3 years ago by Peter Langfelder ★ 3.0k • written 6.3 years ago by bekah ▴ 40

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RNA-seq WGCNA package soft power

6.4 years ago modarzi ▴ 10

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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…

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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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