Bioconductor Deseq

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350

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DESeq2 deseq

3 months ago Meme • 0

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353

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deseq DESeq2

updated 5 months ago by ATpoint ★ 4.2k • written 5 months ago by Hugo • 0

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549

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deseq DESeq2

6 months ago georgii.vdovin • 0

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402

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Deseq DESeq2

updated 6 months ago by Michael Love 42k • written 6 months ago by georgii.vdovin • 0

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687

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Z-score RNASeqData Deseq DESeq2

updated 8 months ago by James W. MacDonald 66k • written 8 months ago by khaserdene99 • 0

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1.0k

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DESeq DESeq2

updated 9 months ago by ATpoint ★ 4.2k • written 9 months ago by Abir.khazaal ▴ 10

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679

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DESeq2 apeglm DESeq ApeGLM Ashr

updated 10 months ago by Michael Love 42k • written 10 months ago by Ndimensional ▴ 20

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26k

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deseq deseq2

updated 9 months ago by Erika • 0 • written 9.3 years ago by c.lieftink@nki.nl ▴ 40

8 results • Page 1 of 1

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Answer: Normalisation using clinical traits in RNA seq using DESeq2 by ATpoint ★ 4.2k

See the vignette, it's a FAQ: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-st…

Comment: More regions in union when increasing DBA$config$mergeOverlap by Ian D. ▴ 70

Please could you comment on this @rory

Comment: Using featureCounts with SAF annotation file gives "Error: only GTF files contai by Wei Shi ★ 3.6k

Your bam file names should be stored in a vector and then provided to the `files` parameter.

Comment: Volcano plot of scRNA-seq data not "centered" by Michael Love 42k

Agree with @atpoint Depending on the "groups" in single cell, the question of DE can be not well defined without inserting additional inf…

Answer: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k

Sounds like a normalization problem, but I am not sure how to help with that. Indeed you can use control genes, for example use the top 20%…

Votes

Answer: Not able to install any Bioconductor 3.18 package [unable to access index]

Answer: Documenting resources in an `ExperimentHub` package?

Answer: Not able to install any Bioconductor 3.18 package [unable to access index]

Seurat/DESeq2 - single cell RNA-seq differential expression

Seurat to SingleCellExperiment Converting error in MAC

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