Bioconductor Batch Correction

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1.8k

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scrna-seq integration batch correction

updated 4.8 years ago by Aaron Lun ★ 28k • written 4.9 years ago by p.joshi ▴ 40

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1.2k

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methylation ComBat Linear models batch correction AIC

updated 5.0 years ago by Kevin Blighe ★ 4.0k • written 5.0 years ago by lucasmiranda42 • 0

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762

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DESeq2 batch correction

updated 5.0 years ago by James W. MacDonald 67k • written 5.0 years ago by MT ▴ 10

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1.1k

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Diffbind ATAC batch correction blocking factor

updated 5.3 years ago by Rory Stark ★ 5.2k • written 5.3 years ago by rm1238 • 0

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1.1k

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deseq2 differential expression batch correction design

updated 5.4 years ago by Michael Love 42k • written 5.4 years ago by wunderl ▴ 40

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1.6k

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deseq2 differential expression batch correction

updated 5.4 years ago by Michael Love 42k • written 5.4 years ago by wunderl ▴ 40

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2.1k

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SC3 Scater Scran scRNA-Seq Batch Correction

updated 5.6 years ago by Vladimir Kiselev ▴ 150 • written 5.6 years ago by hamza_karakurt ▴ 60

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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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