Bioconductor DEGraph

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RNASeqData DEGraph RNASeq edgeR DegNorm

written 9 months ago by Shaozhen • 0

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rnaseqGene edgeR DEGraph DifferentialExpression

updated 13 months ago by Gordon Smyth 52k • written 13 months ago by z_bahari • 0

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GO DEGraph GO DEGraph

14.2 years ago Dick Beyer ★ 1.4k

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Pathways Network SPIA DEGraph Pathways Network SPIA DEGraph

updated 14.2 years ago by January Weiner ▴ 370 • written 14.2 years ago by laurent jacob ▴ 100

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Comment: How to left_join a tidySummarizedExperiment with a GRanges object by seqnames an by James W. MacDonald 68k

Have you figured out how to do this using tidy grammar? Using non-tidy grammar is quite simple, and perhaps you already know how to do that…

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…

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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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