Bioconductor BayesPeak

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BayesPeak bug

8.7 years ago balwierz ▴ 40

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bayespeak

9.7 years ago Reed ▴ 10

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 9.9 years ago by Gordon Smyth 52k • written 10.0 years ago by samuel collombet ▴ 140

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ChIPSeq chipseq BayesPeak ChIPSeq chipseq BayesPeak

12.6 years ago John linux-user ▴ 210

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AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno

12.7 years ago Julie Zhu ★ 4.3k

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BayesPeak BayesPeak

13.7 years ago Mary Ellen Fitzpatrick ▴ 20

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ChIPSeq GO BSgenome BSgenome chipseq BayesPeak ChIPSeq GO BSgenome BSgenome chipseq

updated 13.8 years ago by Jonathan Cairns ▴ 130 • written 13.8 years ago by Andreia Fonseca ▴ 810

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BayesPeak BayesPeak

updated 14.5 years ago by Jonathan Cairns ▴ 130 • written 14.5 years ago by Binbin Liu ▴ 30

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1.9k

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BayesPeak BayesPeak

updated 14.9 years ago by Jonathan Cairns ▴ 130 • written 14.9 years ago by Tim Rayner ▴ 270

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Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k

You can use [bioc-run][1] to simplify things as well. [1]: https://github.com/Bioconductor/bioc-run/tree/devel

Comment: How can I correctly use phyloseq with Docker? by James W. MacDonald 68k

You show how you modified the container, but not how you are running it, which is the critical part.

Comment: Discrepancies in normalised count data vs unnormalised by AMgroup • 0

Thank you for your reply. > Per sample all counts are scaled by the same size factor so I strongly assume that something was parsed here …

Comment: Discrepancies in normalised count data vs unnormalised by ATpoint ★ 4.8k

Please show examples using `plotCounts()`. Custom spreadsheets harbor the risk of parsing errors along the way which very often explains wh…

Comment: Cannot extract size factor from DESeq2 analysis by s.malik • 0

Dear Mike, using tximeta and following code, is this fine to extract normalized counts after `sizeFactors(dds)` gives NULL? `dds <- DESeq…

Votes

Answer: How to combine two DESeq2 objects (dds) for analysis

How to combine two DESeq2 objects (dds) for analysis

How can I correctly use phyloseq with Docker?

A: DESeq2::sizeFactors() function does not output the sizeFactor table.

Comment: Filtering after DESeq

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