Bioconductor Time Series

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2.2k

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deseq2 time series time course

updated 3.6 years ago by Michael Love 41k • written 3.6 years ago by bsierieb ▴ 10

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664

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scRNA-seq time series

3.8 years ago Bogdan ▴ 670

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841

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deseq2 rnaseq repeated measures time series design formula

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by Dorien ▴ 10

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867

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transcriptomics gene expression time series plant biology circadian Job

4.6 years ago dezer ▴ 10

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1.5k

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limma microarray time series DEG paired

updated 4.6 years ago by Gordon Smyth 50k • written 4.6 years ago by kawess • 0

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2.0k

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deseq2 Time Series Gene Clustering LRT ATACseq

updated 5.2 years ago by Michael Love 41k • written 5.2 years ago by kaiser.karim • 0

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1.3k

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deseq2 time series remove batch effect

5.2 years ago Nicola • 0

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3.2k

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limma design model.matrix time series splines

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by tleona3 • 0

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1.0k

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limma time series help

updated 5.3 years ago by Aaron Lun ★ 28k • written 5.3 years ago by rm1238 • 0

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1.3k

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deseq2 time series multiple factor design

updated 5.4 years ago by Michael Love 41k • written 5.4 years ago by Jane • 0

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1.8k

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rna-seq time series patient limma-voom

updated 5.6 years ago by Aaron Lun ★ 28k • written 5.6 years ago by aec ▴ 90

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3.2k

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deseq2 ruvseq spike-in time course time series

updated 6.4 years ago by davide risso ▴ 950 • written 6.4 years ago by staceyborrego ▴ 20

12 results • Page 1 of 1

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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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