Bioconductor Ggplot

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DESeq2 ggplot PCA

written 9 months ago by robledoj13 • 0

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ggplot

updated 2.1 years ago by Konstantinos Yeles ▴ 80 • written 2.1 years ago by R_diot • 0

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ggplot dendogram ggtreeExtra clustree ggtree

2.1 years ago christian.dina • 0

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TCseq ggplot

2.9 years ago jochen • 0

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ggplot

3.4 years ago nattzy94 ▴ 20

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ggplot

updated 4.0 years ago by Kevin Blighe ★ 4.0k • written 4.0 years ago by abhisek001 • 0

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ggplot2 ggplot cmplot

6.1 years ago gens8094 • 0

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ggplot cmplot ggplot2

6.1 years ago gens8094 • 0

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edger ggplot

updated 7.6 years ago by Aaron Lun ★ 28k • written 7.6 years ago by mictadlo ▴ 10

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edger ggplot

updated 7.6 years ago by Gordon Smyth 52k • written 7.6 years ago by mictadlo ▴ 10

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ggplot2 ggplot plot

updated 9.3 years ago by James W. MacDonald 68k • written 9.3 years ago by alptaciroglu ▴ 50

11 results • Page 1 of 1

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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…

Comment: Design formula for circadian time-course data for vst() function by Vishnu • 0

Thank you so much for your reply.

Comment: Analyzing TnSeq data with DESeq2 by Tom • 0

[Doncaster Locksmith][1] delivers trusted, efficient security services tailored to your needs. Analyzing TnSeq data with DESeq2 may uncover…

Answer: Design formula for circadian time-course data for vst() function by ATpoint ★ 4.8k

This was asked before: https://support.bioconductor.org/p/9148734/#9148812 Take-home message is that influence is minor, as you see your…

Comment: Filtering after DESeq by caroline.zanchi • 0

... I did it. It does filter out quite a bit of genes : ``` keep <- filterByExpr(dds, group="host_treatment_generation",min.count = 10, mi…

Votes

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

Comment: Filtering after DESeq

A: Normalized counts from DESeq2 results in similar but not equal total read count?

A: DESeq2: Different Dispersions for different sample groups

A: Contrasts & coefficients in limma

Awards • All

Great Question to inzirio ▴ 10