Bioconductor Fdrtool

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p-value FDR DEP

updated 4.4 years ago by António Miguel de Jesus Domingues ▴ 510 • written 5.0 years ago by Alexei Leliavski ▴ 60

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1.5k

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fdrtool

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by Paul • 0

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deseq2 fdrtool apeglm

updated 5.6 years ago by Michael Love 43k • written 5.6 years ago by Paul • 0

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deseq2 rnaseq sva fdrtool ihw

updated 5.7 years ago by Michael Love 43k • written 5.7 years ago by rihards.saksis • 0

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2.1k

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deseq2 mirna fdrtool

updated 6.7 years ago by Robert Castelo ★ 3.4k • written 6.7 years ago by L_K • 0

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deseq2 fdrtool

updated 7.0 years ago by Michael Love 43k • written 7.0 years ago by bioinfo • 0

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deseq2 rnaseq fdrtool

updated 7.1 years ago by Ryan C. Thompson ★ 7.9k • written 7.1 years ago by C T ▴ 140

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pvalue adjusted pvalue fdrtool

updated 7.7 years ago by Michael Love 43k • written 7.7 years ago by hele7 ▴ 20

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3.4k

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fdrtool deseq2

7.9 years ago rrcutler ▴ 70

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8.5k

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deseq2 rnaseq fdrtool dispersion

updated 8.0 years ago by Bernd Klaus ▴ 610 • written 8.1 years ago by rrcutler ▴ 70

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2.8k

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deseq2 fdrtool genomicalignments

updated 8.1 years ago by Michael Love 43k • written 8.1 years ago by jakob.petereit ▴ 20

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rnaseq deseq2 fdrtool differential gene expression

8.2 years ago tcalvo ▴ 100

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2.9k

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fdrtool p-value distribution

8.7 years ago j.bergenstrahle ▴ 90

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deseq2 FDR fdrtool

updated 8.7 years ago by Bernd Klaus ▴ 610 • written 8.7 years ago by deena ▴ 20

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deseq2 multiple factor design FDR fdrtool

updated 8.8 years ago by Michael Love 43k • written 8.8 years ago by marieke • 0

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deseq2 fdrtool

updated 9.4 years ago by Bernd Klaus ▴ 610 • written 9.4 years ago by dhibar ▴ 60

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2.7k

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deseq2 rnaseq contrast multiple comparisons fdrtool

9.5 years ago sebastiano.curreli • 0

17 results • Page 1 of 1

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Comment: Getting a large intercept with DESeq2 by Michael Love 43k

Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…

Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k

As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…

Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k

The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …

Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k

There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…

Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k

Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…

Votes

Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif

Using edgeR or DESeq2 to analyze allele-specific expression?

Answer: DESeq2 design for haplotype MPRA

Answer: Failure to download resources (MeSHDb) from AnnotationHub

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Popular Question to Stephen Piccolo ▴ 600