Bioconductor Contrasts

Showing : Contrasts • reset

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3.4k

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DifferentialExpression contrasts interaction DESeq2

written 2.0 years ago by Nicole ▴ 10

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2.1k

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DifferentialExpression DESeq2 contrasts

3.0 years ago • updated 2.9 years ago Jane ▴ 10

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1.4k

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edger limma design contrasts batch

updated 5.1 years ago by Aaron Lun ★ 28k • written 5.1 years ago by Pietro ▴ 40

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1.4k

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deseq2 deseq differential expression contrasts

updated 4.5 years ago by Michael Love 41k • written 4.5 years ago by Keith Hughitt ▴ 180

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1.3k

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contrasts limma voom

updated 2.2 years ago by Gordon Smyth 50k • written 2.2 years ago by S T ▴ 90

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1.2k

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edger limma contrasts DGE

updated 4.4 years ago by James W. MacDonald 65k • written 4.4 years ago by s.connell • 0

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1.1k

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edger contrasts

updated 5.2 years ago by Gordon Smyth 50k • written 5.2 years ago by Maiv • 0

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1.1k

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DESeq2 RNA-Seq Multifactorial Design GLM Contrasts

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by ananda2 • 0

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1.0k

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deseq2 contrasts reference level

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by ananda2 • 0

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1.0k

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DESeq2 phyloseq contrasts

updated 2.8 years ago by Kevin Blighe ★ 3.9k • written 2.8 years ago by Mir • 0

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996

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edgeR contrasts limma design model.matrix

16 months ago mohammedtoufiq91 ▴ 10

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987

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limma nanostring contrasts

updated 4.6 years ago by Gordon Smyth 50k • written 4.6 years ago by uridavid.akavia • 0

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970

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topTable voom contrasts

2.7 years ago James • 0

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732

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DESeq2 contrasts

updated 2.3 years ago by Michael Love 41k • written 2.3 years ago by Mir • 0

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682

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edger contrasts model.matrix circadian

4.4 years ago ingerslev • 0

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679

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deseq2 multiple factor design contrasts experimental design

updated 4.9 years ago by Michael Love 41k • written 4.9 years ago by kehoe • 0

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667

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limma F-statistic contrasts

updated 18 months ago by Gordon Smyth 50k • written 18 months ago by jeltje.van.baren • 0

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664

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MultipleComparison DESeq2 Genetics contrasts RNASeq

updated 9 months ago by James W. MacDonald 65k • written 10 months ago by a26fd14e • 0

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564

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contrasts DESeq2

11 months ago • updated 10 months ago jovel_juan ▴ 30

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294

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design edgeR contrasts

updated 6 weeks ago by Gordon Smyth 50k • written 6 weeks ago by JKim • 0

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223

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DESeq2 contrasts

updated 6 days ago by ATpoint ★ 4.1k • written 6 days ago by bioinf ▴ 10

21 results • Page 1 of 1

Recent ...

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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p- by Chris • 0

Thanks Gordon for the advice! I ran fgsea, gsva and camera(), the most significant pathways are different. For the purpose of finding pathw…

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 41k

Check the number of bootstrapped data per chromosome compared to the original, and then you can also look at its distribution. For this it'…

Comment: DNAString: Standard checksum function? by Henrik Bengtsson ★ 2.4k

For completeness: SEGUID v2 (https://www.seguid.org/), implemented in CRAN package **[seguid](https://cran.r-project.org/package=seguid)*…

Comment: fgsea significant result by Chris • 0

Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…

Comment: SGSeq: moving toward diffex from SGSeq analysis by Sara • 0

Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Handling multiple differential expression comparisons

Answer: fgsea significant result

package goseq seems to be not available on the latest version of R

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