Bioconductor Time-series

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2.8k

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deseq2 time-series design matrix edger

updated 5.2 years ago by Michael Love 41k • written 5.2 years ago by Assa Yeroslaviz ★ 1.5k

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1.3k

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deseq2 timecourse multiple time points time-series

updated 5.8 years ago by Michael Love 41k • written 5.8 years ago by zhangfei-123 • 0

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1.5k

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DESeq2 time-series

updated 6.5 years ago by Michael Love 41k • written 6.5 years ago by gtechbio ▴ 10

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916

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time-series DESeq2 RNASeq timecoursedata TimeCourse

updated 8 months ago by ATpoint ★ 4.1k • written 8 months ago by Debebe • 0

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1.9k

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deseq2 cancer rna-seq time-series

4.8 years ago mah19 • 0

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618

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DESeq2 time-series timecoursedata timecourse multifactorial

updated 17 months ago by Michael Love 41k • written 18 months ago by arshad1292 • 0

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820

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half-life DESeq2 time-series

updated 3.1 years ago by Michael Love 41k • written 3.1 years ago by Xianjun Dong ▴ 10

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787

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time-series mfuzz replace=FALSE

23 months ago soda ▴ 80

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1.0k

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deseq2 time-series without replicate

updated 5.8 years ago by Michael Love 41k • written 5.8 years ago by bahlv • 0

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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0

Thank you Tim, this is a great help in getting me started!

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Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

A: Print Differentially Expressed Exons From Dexseq Results

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