Bioconductor DEs

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281

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DESeq2 des

updated 5 months ago by James W. MacDonald 67k • written 5 months ago by Atul K. • 0

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967

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 7 months ago by James W. MacDonald 67k • written 7 months ago by Alexandre • 0

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293

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Des DESeq2

updated 7 months ago by hemantcnaik • 0 • written 7 months ago by Sahar • 0

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476

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DESeq2 DEs

8 months ago feather-W • 0

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671

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DESeq2 des

updated 2.0 years ago by Michael Love 43k • written 2.1 years ago by Devin • 0

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735

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DES DESIGN

updated 2.2 years ago by Michael Love 43k • written 2.2 years ago by mike • 0

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829

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DESeq2 DES

updated 3.9 years ago by Michael Love 43k • written 3.9 years ago by heikki.sarin ▴ 10

7 results • Page 1 of 1

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Answer: scuttle::perFeatureQCMetrics runs very slow for big scRNA-seq data by Aaron Lun ★ 28k

You don't mention how your matrix data is being represented, but if it's a file-backed matrix (e.g., `HDF5Matrix` or one of its variants, b…

Comment: contrast matrix design for a continuous variable by dtzhu337 • 0

Thank you, Gordon. X is time splines for time point, and yes, it's needed. However, I was also thinking to incorporate time point with se…

Answer: contrast matrix design for a continuous variable by Gordon Smyth 52k

Yes, the design and contrasts are correct. Your analysis is also adjusted for covariates defined by X, which I assume is what you want to …

Comment: fail to use addPerROIQC in Rmd by liu.n • 0

That's odd. So it can run successfully within markdown but would be failed when knitting?

Comment: fail to use addPerROIQC in Rmd by joseph.joonsang • 0

> dim(spe) [1] 19962 425

Votes

Answer: contrast matrix design for a continuous variable

A: What's the difference between p.adjust and qvalue?

Answer: DESeq2- merging technical vs biological replicates

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

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Popular Question to Ou, Jianhong ★ 1.3k