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886

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downloads http429 http Bioconductor

15 months ago shepherl 4.2k

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import.bw rtracklayer Windows http

4.0 years ago sla • 0

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6.3k

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import.bw rtracklayer http RStudio

updated 5.0 years ago by Michael Lawrence ★ 11k • written 5.0 years ago by Søren • 0

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1.6k

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genomicdatacommons tcga gdc rest http

updated 6.8 years ago by Sean Davis 21k • written 6.8 years ago by mk ▴ 20

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gviz gviz-package rtracklayer http

7.8 years ago enricoferrero ▴ 680

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3.8k

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arrayexpress xml rcurl http EBI

updated 8.1 years ago by Wolfgang Huber ★ 13k • written 8.1 years ago by Bernd Klaus ▴ 610

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2.5k

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security http source installation

updated 10.4 years ago by Dan Tenenbaum ★ 8.2k • written 10.4 years ago by will.townes • 0

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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…

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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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