Bioconductor Differential exon usage

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2.8k

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edger normalization differential exon usage splicing

updated 4.1 years ago by Yunshun Chen ▴ 880 • written 4.1 years ago by oakhamwolf • 0

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1.6k

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DEXSeq differential exon usage

updated 6.5 years ago by Alejandro Reyes ★ 1.9k • written 6.5 years ago by A ▴ 40

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differential exon usage exon array analysis annotation hta2.0 diffsplice

updated 7.2 years ago by James W. MacDonald 67k • written 7.2 years ago by relathman ▴ 20

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egdeR multiple time points model.matrix differential exon usage model

7.3 years ago heikki.sarin ▴ 10

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dexseq differential exon usage

updated 7.8 years ago by mat.lesche ▴ 110 • written 7.8 years ago by Assa Yeroslaviz ★ 1.5k

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dexseq differential exon usage

7.8 years ago fizer ▴ 40

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deseq2 dexseq rnaseq differential gene expression differential exon usage

updated 7.9 years ago by Michael Love 42k • written 7.9 years ago by fizer ▴ 40

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896

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dexseq deseq2 differential exon usage

8.1 years ago ste.depo ▴ 10

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dexseq rsem differential exon usage differential gene expression

updated 8.4 years ago by James W. MacDonald 67k • written 8.4 years ago by Assa Yeroslaviz ★ 1.5k

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DEXSeq timecourse rna-seq differential exon usage

updated 8.8 years ago by Alejandro Reyes ★ 1.9k • written 8.8 years ago by MedwayC • 0

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DEXSeq differential exon usage exon usage

updated 9.0 years ago by Alejandro Reyes ★ 1.9k • written 9.0 years ago by biominer ▴ 10

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dexseq rnaseq differential exon usage

9.3 years ago arom2 • 0

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dexseq bitseq cuffdiff Differential exon usage isoforms

9.5 years ago • updated 9.4 years ago elle ▴ 10

13 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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