Bioconductor Bigwig

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1.9k

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DESeq2 edgeR bigwig limma

2.1 years ago • updated 22 months ago Bogdan ▴ 670

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2.1k

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bedgraph wiggleplotr bigwig wig

updated 2.2 years ago by complaintguide • 0 • written 2.2 years ago by Bogdan ▴ 670

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1.7k

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bigWig RNASeqData

2.8 years ago bas_work ▴ 30

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2.0k

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software error BigWig import windows

4.7 years ago • updated 4.6 years ago lsilva.m • 0

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2.1k

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wiggleplotr bigwig coverage ngs

updated 7.1 years ago by kaur.alasoo ▴ 30 • written 7.1 years ago by borgmichael • 0

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3.4k

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bigwig rtracklayer import granges grangeslist

updated 7.3 years ago by Michael Lawrence ★ 11k • written 7.3 years ago by Assa Yeroslaviz ★ 1.5k

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1.3k

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rtracklayer bigwig import

updated 8.0 years ago by Michael Lawrence ★ 11k • written 8.0 years ago by zx8754 ▴ 10

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1.5k

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bigwig rtracklayer export.bw

updated 8.1 years ago by Michael Lawrence ★ 11k • written 8.1 years ago by story.benjamin ▴ 20

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2.6k

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rtracklayer bigwig

updated 8.8 years ago by laurent.lacroix ▴ 30 • written 8.8 years ago by koneill ▴ 30

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1.4k

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rtracklayer BigWig

updated 9.0 years ago by Michael Lawrence ★ 11k • written 9.0 years ago by dborgesrmit • 0

10 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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