Bioconductor Time series

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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

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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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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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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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1.8k

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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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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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1.3k

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deseq2 time series remove batch effect

5.2 years ago Nicola • 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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1.0k

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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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866

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transcriptomics gene expression time series plant biology circadian Job

4.6 years ago dezer ▴ 10

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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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662

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scRNA-seq time series

3.8 years ago Bogdan ▴ 670

12 results • Page 1 of 1

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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!

Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k

Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…

Answer: Too many significant genes when integrating gtex and tcga by James W. MacDonald 65k

See `?results`, in particular the lfcThreshold argument.

Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k

You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…

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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

stuck on unimplemented type 'list' in 'EncodeElement'

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