Bioconductor ChIP-seq

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next-generation sequencing rna-seq chip-seq single cell Job

9.5 years ago Katja Hebestreit ▴ 130

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diffbind chip-seq

updated 9.8 years ago by AB ▴ 110 • written 10.8 years ago by medinaale • 0

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diffbind chip-seq bam

10.1 years ago eli7javasky • 0

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chipseq chipqc chip-seq

10.2 years ago lindahove ▴ 10

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Course RNA-Seq Chip-seq Parallel News

10.7 years ago Martin Morgan 25k

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csaw chip-seq clip-seq

10.8 years ago IV ▴ 30

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DiffBind ChIP-Seq

updated 11.0 years ago by Rory Stark ★ 5.2k • written 11.0 years ago by Georg Otto ▴ 120

57 results • Page 2 of 2

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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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Popular Question to Stephen Piccolo ▴ 600