Bioconductor Hub Genes

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WGCNA eigengene hub genes

7.0 years ago yifangt ▴ 20

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wgcna rbgl graph coexpression hub genes

updated 8.6 years ago by Peter Langfelder ★ 3.0k • written 8.6 years ago by Alan Smith ▴ 150

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wgcna visant module hub genes

updated 8.7 years ago by etycksen • 0 • written 8.7 years ago by agattorosso • 0

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WGCNA Hub Genes KmE Intramodular Connectivity

updated 9.4 years ago by Peter Langfelder ★ 3.0k • written 9.4 years ago by brohawndg ▴ 150

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Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k

You will probably have to ask the Signac people. I don't know exactly what is going on under the hood for `AddMotif`, but the `EnsDb` seems…

Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by Paul • 0

Unfortunately I've updated my code with the newest GRCm39 genome, and yet I am still getting the same error.... Is there anything else I ca…

Comment: WGCNA with TPM tables by ATpoint ★ 4.5k

WGCNA is not a Bioconductor package, but generally: If you want to do serious analysis then find the raw data. There is no guarantee what …

Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k

The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…

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…

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Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (

Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (

Comment: does anyone how to create rarefaction curves from a phyloseq object?

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

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