Bioconductor JunctionSeq

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DEXSeq JunctionSeq RNAseq QoRTs

3.9 years ago n.tear ▴ 20

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junctionseq splicing RNAseq DEXSeq

5.2 years ago stuart ▴ 10

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954

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JunctionSeq

7.8 years ago rachelrodgers12 • 0

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968

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junctionseq relevel reference

7.9 years ago Assa Yeroslaviz ★ 1.5k

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junctionseq qorts multiple factor design relevel

8.0 years ago Assa Yeroslaviz ★ 1.5k

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deseq2 junctionseq dexseq estimatedispersions rnaseq

updated 8.1 years ago by Steve Lianoglou ★ 13k • written 8.1 years ago by l.frank • 0

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957

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junctionseq

8.2 years ago jbono ▴ 10

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junctionseq design and contrast matrix

8.3 years ago stuart • 0

8 results • Page 1 of 1

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Answer: Selection of correct coefficients or contrasts in DESeq2 by swbarnes2 ★ 1.4k

I think you need to include the design you used, and the command you used to call it. The simplest answer is that your two ways of doing t…

Comment: Csaw normalization strategies - general inquiry by Luca • 0

Hello Aaron, About the IP efficiencies, yes definitely and for us, to complicate this experiment further, these batches were generated by …

Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by Quang NN ▴ 10

Thank you ATpoint for your response. In bulkRNAseq, I did have two cell types to compare. But, I want to also see if bulkRNAseq might have …

Answer: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k

The choice of variable genes is typically part of a QC process. You select genes that in an unbiased fashion (unbiased because variance cal…

Comment: How to compare expression levels of genes between scRNAseq and bulkRNAseq? by ATpoint ★ 4.6k

My take is that RNA-seq (be it bulk or single-cell) is inherently relative. I don't think you can really "compare" the absolute expression …

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Answer: Csaw normalization strategies - general inquiry

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

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