Bioconductor Pcatools

Showing : pcatools • reset

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244

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COTAN PCAtools

10 months ago Silvia • 0

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1.1k

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DESeq2 eigencorplot PCAtools

18 months ago BioinfGuru ▴ 70

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725

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DESeq2 PCAtools

updated 18 months ago by Michael Love 43k • written 18 months ago by Aaliya • 0

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2.7k

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DESeq2 RSTUDIO PCAtools

updated 18 months ago by swbarnes2 ★ 1.4k • written 19 months ago by Aaliya • 0

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2.2k

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edgeR PCAtools

written 19 months ago by Fabian • 0

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6.1k

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ellipse RNAseq PCAtools

updated 2.6 years ago by CP • 0 • written 4.5 years ago by elizabethe819 • 0

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2.0k

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Biplot FactoMineR proteomics PCAtools ellipse

updated 2.8 years ago by Kevin Blighe ★ 4.0k • written 2.8 years ago by M Tuhin • 0

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2.0k

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illumina PCAtools PCA

updated 3.0 years ago by Kevin Blighe ★ 4.0k • written 3.0 years ago by ilaria.debenedictis • 0

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1.3k

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PCAtools bioconductor

updated 3.3 years ago by James W. MacDonald 68k • written 3.3 years ago by pterry • 0

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2.4k

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PCAtools pcaExplorer pcaMethods

updated 3.4 years ago by Federico Marini ▴ 180 • written 3.4 years ago by m610110001 • 0

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4.2k

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PCAtools edgeR pcaExplorer RNASeq RNAseq123

3.6 years ago Alan • 0

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1.4k

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PCAtools

4.6 years ago luca.s ▴ 50

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4.0k

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PCAtools

updated 4.8 years ago by Kevin Blighe ★ 4.0k • written 4.8 years ago by Terra • 0

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4.5k

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biplot PCA RNASeq PCAtools

updated 4.9 years ago by Kevin Blighe ★ 4.0k • written 4.9 years ago by mschmidt ▴ 10

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2.5k

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PCAtools biplot DESeq2 RNASeq PCA

updated 5.0 years ago by Kevin Blighe ★ 4.0k • written 5.0 years ago by ecg1g15 ▴ 30

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2.1k

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PCATools

updated 5.1 years ago by Kevin Blighe ★ 4.0k • written 5.1 years ago by oakhamwolf • 0

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2.5k

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EDA pcaExplorer PCAtools PCA

updated 3.9 years ago by Miguel ▴ 20 • written 5.2 years ago by k.vitting.seerup ▴ 120

17 results • Page 1 of 1

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Replies

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