Bioconductor Rory Stark

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diffbind rory stark chip seq

updated 2.9 years ago by Rory Stark ★ 5.0k • written 3.4 years ago by bioinfouser2 ▴ 10

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CHIPQC Diffbind chipseq rory stark Thomas Carroll

updated 13 months ago by arisarkar88 ▴ 40 • written 3.4 years ago by bioinfouser2 ▴ 10

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diffbind Rory Stark coordinate

updated 3.5 years ago by Rory Stark ★ 5.0k • written 3.6 years ago by Guandong Shang ▴ 40

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diffbind rory stark

6.2 years ago andrew.gehrke • 0

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diffbind chipseq atac-seq rory stark

updated 6.5 years ago by Rory Stark ★ 5.0k • written 6.5 years ago by andrew.gehrke • 0

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rory stark

6.8 years ago • updated 6.3 years ago mforoo1 • 0

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Rory Stark diffbind TMM edgeR chipseq

updated 7.2 years ago by Rory Stark ★ 5.0k • written 7.4 years ago by akdess • 0

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Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

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Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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