Bioconductor Cuffdiff

Showing : cuffdiff • reset

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546

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cummeRbund cufflink cuffdiff

updated 21 months ago by James W. MacDonald 68k • written 21 months ago by sumitra • 0

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3.8k

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RNA-seq / XLOC cuffdiff

updated 3.3 years ago by Lan • 0 • written 5.0 years ago by mg.mahabad1365 • 0

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1.9k

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WGCNA cuffdiff

6.6 years ago sbbinfo90 • 0

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1.5k

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cuffdiff sqlite

7.4 years ago handgabriel • 0

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1.5k

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kegg readcufflinks cuffdiff cuff

updated 7.5 years ago by thokall ▴ 160 • written 7.5 years ago by pierre.biojoux • 0

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4.0k

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htseqtools deseq2 counts cuffdiff

9.2 years ago Jon Bråte ▴ 260

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1.8k

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GAGE Cuffdiff gene names

updated 9.4 years ago by Luo Weijun ★ 1.6k • written 9.4 years ago by user31888 ▴ 30

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2.3k

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SpliceR Cuffdiff

updated 9.6 years ago by deppt002 • 0 • written 9.9 years ago by mfahim • 0

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1.7k

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deseq2 cuffdiff differential gene expression

9.8 years ago Assa Yeroslaviz ★ 1.5k

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4.0k

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dexseq bitseq cuffdiff Differential exon usage isoforms

9.9 years ago elle ▴ 10

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1.9k

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deseq2 cuffdiff

updated 9.9 years ago by Michael Love 43k • written 9.9 years ago by a.de-giorgio12 • 0

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2.0k

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cummeRbund Script analysis RNAseq cuffdiff

updated 10.0 years ago by andrew.j.skelton73 ▴ 370 • written 10.0 years ago by mfahim • 0

12 results • Page 1 of 1

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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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