Bioconductor ColData

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748

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DESeq2 design coldata

updated 8 months ago by swbarnes2 ★ 1.4k • written 8 months ago by arfranco ▴ 130

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849

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ColData pheatmap DESeq2

written 18 months ago by dania.khalid • 0

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1.5k

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SingleCellExperiment colData rename

updated 22 months ago by Basti ▴ 780 • written 22 months ago by achoppe ▴ 10

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BiSeq Coldata

4.6 years ago akhaira • 0

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deseq2 levels factor colData

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by ariel ▴ 20

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47k

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deseq2 coldata

updated 6.1 years ago by swbarnes2 ★ 1.4k • written 6.1 years ago by mjrarcher ▴ 10

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variantannotation coldata

updated 6.3 years ago by Valerie Obenchain ★ 6.8k • written 6.3 years ago by lvclark ▴ 10

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deseq2 coldata NA

updated 4 months ago by Michael Love 43k • written 6.4 years ago by t.kuilman ▴ 170

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1.7k

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multiassayexperiment colData

updated 7.1 years ago by Levi Waldron ★ 1.1k • written 7.1 years ago by Lluís Revilla Sancho ▴ 760

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Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…

Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k

I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…

Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

They provide the code they used for DGE analysis in a gitlab link that can be found in the paper. In there you can find: ```` # estimate d…

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C: How does edgeR cpm function calculate log(CPM) values?

Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis

scater/scran with TPMs from Salmon - counts?

A: Full length single-cell RNA-seq - tximport output for downstream analysis

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