Bioconductor Bayespeak

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BayesPeak bug

9.1 years ago balwierz ▴ 40

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bayespeak

10.1 years ago Reed ▴ 10

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 10.3 years ago by Gordon Smyth 53k • written 10.3 years ago by samuel collombet ▴ 140

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ChIPSeq chipseq BayesPeak ChIPSeq chipseq BayesPeak

13.0 years ago John linux-user ▴ 210

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AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno

13.1 years ago Julie Zhu ★ 4.3k

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BayesPeak BayesPeak

14.0 years ago Mary Ellen Fitzpatrick ▴ 20

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ChIPSeq GO BSgenome BSgenome chipseq BayesPeak ChIPSeq GO BSgenome BSgenome chipseq

updated 14.2 years ago by Jonathan Cairns ▴ 130 • written 14.2 years ago by Andreia Fonseca ▴ 810

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BayesPeak BayesPeak

updated 14.8 years ago by Jonathan Cairns ▴ 130 • written 14.8 years ago by Binbin Liu ▴ 30

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BayesPeak BayesPeak

updated 15.3 years ago by Jonathan Cairns ▴ 130 • written 15.3 years ago by Tim Rayner ▴ 270

9 results • Page 1 of 1

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Answer: Can I set the normalizationFactors of DEseq2 object as 1 after using RUVg? by Michael Love 43k

I'm not familiar with this usage, or code here ``` normFactors <- exp(-1 * offst(set2)) ``` In the RNA-seq gene-level workflow, we …

Answer: Which of apeglm and ashr may be more appropriate for pseudobulked DESeq2 analysi by Michael Love 43k

> apeglm appears much more aggressive in shrinkage, pushing many genes toward logFC = 0 > ashr maintains a gradient of shrinkage val…

Comment: voomLmFit fitted log-CPM values by Gordon Smyth 53k

The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…

Comment: voomLmFit fitted log-CPM values by Lina ▴ 10

Is the output from fitted(v) in the log2 CPM scale? or CPM scale?

Answer: voomLmFit fitted log-CPM values by Gordon Smyth 53k

Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```

Votes

A: How barcode-plot enrichment is calculated?

Answer: ROAST compare results with complex design

How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?

Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea

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